How to use trains in Japan
I feel like Japan is a wonderful country for backpackers : it's so safe, cheap and easy to move from a city to another thanks to Japan railroads. Look at this handy map of Kansai area railroads, it's so impressive how dense it is. The only places you can't go by train are lost in the mountains ... Now that I'm used to live here I can't think about going somewhere without using train (or my bicycle of course ;-) ). However there are some 'traps' for the foreigner due to japanese trains particularities. Actually, maybe there aren't compare to your own country, but at least compare to France there are some major differences leading easily to confusion. So, just in case, let me introduce you how to travel by train in Japan...
1) First Step : Find how to go from A to B ?
When I look for my way I always use the wonderful Hyperdia website. It finds itinerary between two stations and describes fees, delay, eventual transfers and time to wait, name of the train line (private companies are included), maps and others useful informations. It even finds itinerary using other means than train if necessary (foot, boat, bus, ...). That's definitely the Bible for Japan transportations itinerary and time schedule !
There, take good care at the line name. In Japan there is not only the national railroad company Japan Rail, but a lot of local private companies (Hankyu, Keihan, Hanshin, etc...). Depending on the place you go you will use one or the other, so keep in mind the name of the station AND the name of the line to avoid confusion. Some stations have the same name but are at different places depending on the company, some others have different names depending on the company but are at the same place. Moreover different cities often have the same name. Be careful when you select departure and destination location !
Lets have a look at screenshots.
If the name of destination (or departure) you entered can't be found you will see this message. Just come back to the previous page and check for the writing of the name of departure and destination.
If everything goes right you will arrive on this page. On the first line you can choose the date of departure or arrival or "around (what time you want to travel)". The second, third and fourth lines shows your departure and destination. If several places has the same name you can select which one in a list has shown below :
On the fifth line you find : how many answers you want to display (if you've chosen "departure" on the first line it's the X trains departing from the time selected, if it was "arrival" it's the X trains arriving before the time selected); the type of seat you want (reserved or not, ...); the type of transportation you want/don't want to use.
Once everything is as you wish you can click on the "start" button.
Then the list of matching itinerary is displayed. You have a brief summary on the top of the page and you can click on each line to reach directly the corresponding itinerary detailed lower.
For a simple itinerary it looks like the screen shot above. You have first the time required, the distance in kilometer and the fare. Following, the detail of the itinerary with time, name of station, name of line, cost of each section. If you click on the icon in the timetable column in front of a station name you will display the timetable of all the train stopping at this station on the selected day. If you click on the one in front of a line name, you will display the timetable of all the train running on this line for the selected section. You can also find there the number of each train, the detail of distance between stations, boarding platform number, each served stations and time it stops at. On both timetable your train is highlighted to make it easy to find it. If you click on the icon in the information column you will have the detail of the journey for the selected train : train number, detailed distances, stops, stops delay, platform number at each station. In the following columns you can find a links toward reservation tools for trains or planes requiring a reservation (like Shinkansen), link toward car renting services and hostel booking engine, and link toward a map.
If your itinerary is a little bit more complex with several changes and transportation means it's just the same but a little bit longer :
In the first column you also have the transfer time between two trains. Don't forget to check it to be sure you have enough time to change platform with your big backpack ! ;-)
2) Second step : Buy your ticket and enter the station !
Ok now you've found your way and you went at the station.
First case : you are a happy Japan Rail Pass holder.
Sky is blue, sun's shining, birds' singing for you in the trees and your life is a paradise. Just show your pass at the employee near the gate and enter the station.
And don't forget : you have to buy your Japan Rail Pass BEFORE you enter Japan, in your own country. You CAN'T buy it once you're here !!
Second case : any cases different from the first one.
You're an adventurer, you want to fight with the frightening 'salalyman', to have your unknown neighbour sleeping on your shoulder, get crushed on the window by a smily white gloved employee, attacked by a old woman, and wonder why the hell all passengers suddenly get off from you train to immediately get into the one waiting on the other side of the platform while both appears bounded for the same journey... you're a real backpacker ! ;-)
This adventure starts at the gate with the question : how do I buy my ticket ?
You may be scared by the board of the vending machine and choose the counter. In this case printing the page of your journey found on Hyperdia would be a good idea unless you speak a little bit of japanese.
If you prefer the vending machine, actually it's not so difficult except for the Shinkansen. But in Shinkansen station there will always be someone speaking few words of english to help you anyway. The basic way to buy using the machine is :
1) find the cost of your journey on the big board above your head (once again checking for that before with Hyperdia would be helpful). This is the number written below the name of your destination station (the name of main stations is also written in alphabet). The cost is based on the distance between your departure and your arrival, with no consideration for distance really covered. Some people enjoy a trip around big cities having a loop line for the cheapest cost of one station to the following one on the opposite direction. You can even make the whole loop several time if you really love it !
2) insert coins or bills in the machine until you reach the amount required. Machines always give the change and accept bills, but not credit cards ! Buttons with different amounts light up, press the one with the right amount and take your ticket and your change.
That's simple, isn't it ? And even if you mistook the cost of your journey, don't worry. When you will exit at destination, the employee at the gate will help you to regularize your situation and you won't be charge for penalty.
On this typical machine you can see : a bunch of little black buttons, they will light up showing selectable fares as one goes along you insert money; at the left of these buttons small white ones to select how many passengers; down in the middle the hole to insert bills and immediately at its right the hole for the coins; at the bottom the repository for ticket and your change.
Once you've got the ticket, insert it in the gate. If you've got several (it might be the case if you use the Shinkansen for example), insert them all at the same time and don't try to understand the meaning of each one, even after several years here I'm still not sure to have understood ! They/It will get out at the other side of the gate and gate will open. Don't forget to take them back !!! You will need them at the exit. And don't worry if it gets out less tickets than you entered ! At least there must be one, or it means the machine was hungry and you will have to call an employee to help you...
Oh, about the 'gate', if you're used to 2 meters of heavily aggressive and high secured steel doors like in Paris subway, please try to don't laugh loudly at japanese cute plastic saloon gates of 30 cm height ... ;-) Neither try to jump over them or pass without inserting your ticket if there is no door !!!
3) Third step : which train to board in ?
Yatta ! You're inside the station ! Now you have to find your platform number by looking at the electronic board.
If it's written in japanese just wait a little, english translation follows japanese announces. If you are in a smaller station with a mechanical board, names of main stations are also written in alphabet. That's generally enough to find your way. But here comes the beginning of your troubles...
If you use the Shinkansen, in case you have the Japan Rail Pass just take care that you cannot use the Nozomi Shinkansen. Except that, you can board any Shinkansen you wish. If you have a normal ticket, check at the name of your Shinkasen (Hikari, Nozomi, Kodama, ...) and the departure hour and you will find the platform number.
If you use a normal train, you will probably see that several ones depart for your journey. Thinking the earliest the best maybe a mistake. Firstly because you may loose a lot of time. Secondly because you may board on a train that doesn't stop at your station !
The reason is that in Japan transport facilities are wonderfully optimized. For the same journey it exists several types of train stopping at more or less numerous stations between departure and arrival. For example :
普通 (futsuu) : local, stops at every station
準急 (junkyuu) : semi express, stops at 3/4 of the stations
快速 (kaisoku) : rapid express, stops at half the stations
特急 (tokkyuu) : limited express, stops at main stations only
通勤特急 (tsuukin tokkyuu) : special limited express, stops at some main stations only
This is trains types of the Hankyu line between Kyoto and Osaka, which is a heavy loaded traffic line. That's why there is a lot of types of trains. However on small lines you will probably have to choose only between futsuu and something like kaisoku or tokkyuu types, or even futsuu only I think.
All these lines are connected at key stations and trains are synchronized to give you the possibility of optimizing your journey by going quickly to the next key station with a tokkyu train and then change to reach your station with a futsuu train, without loosing time on connection. In some case it's even faster to pass your station a little and come back with a slower train. Now you understand what are doing these Japaneses who change suddenly from a train to another. It's quite a sport to master the best combination if you commute everyday and have others considerations like unbearably crowded special limited express and time you want to stay in your beloved futon ! But for a tourist it probably looks more like a game I think ;-)
By the way, being a tourist with a quite flexible schedule won't save you with certitude from crowded train. Rush hours are quite large so you won't be safe by avoiding train around 8:00 and 17:00 only. You should better consider intervals from 7:00 to 9:00 in the morning, and in the evening it starts at 17:00 and at 22:00 there is still no more places to seat if you travel between Osaka and Kyoto ! So if you want to be sure to have seat, the only solution is to take your time on a slow 'futsuu' and enjoy the landscape ...
On each platform you will find timetable of trains stopping on this platform. Each line corresponds to one hour, the numbers on the lines show the minute the train will stop at the station you are, the color refer to the type of train (look at the bottom to see which color is affected to which train and stations desserved by it), the little symbols indicate the correspondence between two different types of trains on the same line.
4) Fourth step : board the train
May look trivial but ...
On the Shinkansen, there is three kinds of cars : the green car, the reserved seat car, the unreserved seat car. The green car is higher quality of service and of course higher price. The Japan rail pass comes in both type, take care for that. The standard japan rail pass allows you to board in unreserved seat only but of course you can pay a supplement to reserve you seat. If you don't have japan rail pass, I recommend you to don't take a reserved seat. You will save money and it seems to me you will ever be able to have a seat except on some very special periods like Obon or Golden Week.
The type of car is written on it, near the door. Also, you can find a board on the platform, or thanks to electronic display, detailing the car numbers for each type. then just look at the floor and you will find the number of the car you're in front of. If the Shinkansen is not yet here, the location of doors is shown by lines (or symbols) along which you're supposed to queue properly (please !).
On a normal train, you can board almost any car but some have particularities. First, look at the marks on the floor, and do as explained for the Shinkasen. Then check for an important things : if you're the only male in the queue, you're probably attempting to board a "female only car", look at the floor and if you see a sign like the one below you'd better change of queue or a old Japanese lady may try to get you out with her umbrella !!
The point is that this kind of restricted car is not always 'active', for example it can be only during rush hours. But the sign is always here anyway. So if you can't read japanese, to be sure, check for Japanese males in the queue, or change to the next car.
Some cars are also 'non cellular phones' car, where you can't use your phone, but as tourist I doubt you've got one and that's surely why it's not written anywhere in english and you can't understood except if you speak japanese and listen at the conductor instructions. On the Hankyu trains it's the last and the first car, but I don't now about others companies.
Something I particularly appreciate after my parisian life : sometime two platforms surround only one lane, so passengers getting out of the train can go on one side while passengers boarding the train can use the opposite side. No crush !
5) Fifth step : inside the train
There is several type of trains of course, with various arrangement for seats or electronical equipments.
For the one with long seats on each sides you have to take care that they can be fold back on heavy loaded line to open more space and 'charge' more people in the car. As it folds as a whole take care to don't stay the only one seated bothering all the other wanting to fold it up !
The seats oriented in the sens of march also have a trap. Japanese people hate to seat facing the rear of the train (why ?????), thus train company installed automatic seats (on some train, manual on the others) that change direction automatically when the train stops at terminus and go back from where it comes. If you think like Japanese (and at least one French) "train=bed" don't forget to wake up at terminus. The seat won't care if you're still on it and you may have a violent wake up !!
Except that nothing to fear. I would just recommend to avoid crowded train, really not enjoyable, but that's the same everywhere. By the way there is some advices in this situation. Get as much as possible away from the door, that's where you will have a chance to be able to breath ! If you can't seat just stand in front of a lucky seated guy and pray for him to get off at next station, then jump on the freed 30cm of seat while forgetting all rules of politeness toward the old lady beside you. Crowded train is a wargame !
Speaking about politeness, some cute pictures on the wall try to suggest to passengers the polite way to act inside train. Don't read newspaper, don't listen music, put your bag on your knees or between your legs, don't speak, don't use your phone nor your DS Lite, don't make up, ... In a short shot, be a statue, and please a tiny one ! But after one minute you will start to see the myth of the ultra polite and disciplined Japanese starting to collapse. Take it the peaceful way and try to give a good image of foreigners. Instead, enjoy the noisy but funny grand'ma, the unbelievable make up of boys and miniskirts of girls, the sleeping Japaneses falling in indescribable position or using their unknown neighbor as a pillow, or the completely drunk salary man going back home.
6) Sixth step : When to get off ?
During your journey you will hear the conductor speaking with no break. He's telling the name of next stations, connections, rules described above and so on. Even if you can't speak japanese you may be able to catch the name of the station which is clearly repeated when the train stops. If not you can still understand where you are thanks to the name of each stations written on the pillar of the platform in alphabet. In recent trains digital screens have been installed inside each cars and display (between two advertisements) next stations. In this case it's really easy to understand. Also, description of the line is displayed on top of the doors. But you have to know on which type of train you are (explained in 3) ) to read it.
If you miss your stop, don't worry you can get off at the next one and take another train in the opposite direction. Usually both side of the line are connected without having to pass through the gates so you won't have to pay for your mistake (only your starting and arrival points are taken in consideration). But in very small stations you may have to get out of the station to enter again on the opposite side. If so, you will have to pay a supplement because you went to far, and then buy a new ticket to come back ! To avoid that maybe it would be better to wait until the next big station.
7) Seventh step : Get out the station
Enter your ticket in the gate and just pass through. If you lost it or mistook the fare you will be asked (and eventually helped) to regularize your situation thanks to a dedicated machine near the gates or at counter. I even could got back my money once I mistakenly bought a too much expensive ticket.
In front of the gates you will find a lot of useful information like maps of the area, direction for interesting spot in the area, direction for taxi, bus, connection, services, ... Also, in big stations or stations near some place of interest there is almost always a little tourist information center. It maybe very small but the usual old men/woman working there are always extremely helpful. I have great memories of receiving information in fluent french at the foot of Mount Fuji in a so tiny station... !
Board showing direction for exits, transfer points to subway, shinkansen line, toilet, taxi, information center, ...
At last, maybe you want to keep a souvenir of this 'big' adventure ? There is sometime a free for use inking pad in front of the gates. It seems Japaneses love a lot this kind of souvenir !
8) Some others things to know ...
a) Some examples of fare and time
Here comes some examples of journey by train to help you make up your mind about japanese transportation. Fare, frequency and delay are given roughly and without any guarantee. Refer to Hyperdia for detailed and confirmed informations.
By Shinkansen :
Sendai - Tokyo : 2h12mn, 5800 yen without reserved seat, departure every 10mn
Tokyo - Kyoto : 2h20mn, 8000 yen without reserved seat, departure every 10mn
Kyoto - Osaka (ShinOsaka station) : 14mn, 540 yen without reserved seat, departure every 10mn
Osaka (ShinOsaka station) - Hiroshima : 1h27mn, 5500 yen without reserved seat, departure every 10mn
Hiroshima - Fukuoka (Hakata station) : 1h10mn, 5000 yen without reserved seat, departure every 30mn
By normal train :
Tokyo - Mount Fuji (kawaguchiko station) : 2h23mn, 4270 yen, 2 transfers
Tokyo - Kamakura : 1h, 900 yen
Tokyo - Osaka : 9h, 10000yen, 7 transfers
Osaka - Kyoto : 1h, 500 yen
Kyoto - Nara : 1h, 700 yen
Osaka - Kobe : 24mn, 400 yen
Osaka - Himeji : 1h, 1500 yen
Osaka - Hiroshima : 6h, 6000 yen, 3 transfers
Hiroshima - Onomichi : 1h, 1500 yen
Hiroshima - Fukuoka (Hakata station) : 6h, 6000 yen, 4 transfers
b) Discount Ticket
The king of them is of course the Japan Rail Pass. If you want to see a lot of places in Japan on a short period, this is the indispensable solution. This ticket can be bought for one, two, or three weeks. It will never be said enough : take care that it MUST be bought OUTSIDE Japan ! Thanks to it you can use almost all the JR train, as much as you want. The most you use train, the most you save. For example, if you buy a one week JRPass (28300 yen) and schedule a quite typical go and get back from Osaka to Tokyo (14050 yen X 2), it leaves you all the other trips during the week for free ! Easy to make it profitable ...
The official website is here : http://www.japanrailpass.net/eng/en001.html
Another interesting ticket is the 青春18切符 (seishun 18 kippu). It's a special ticket sold only during three periods of the year, corresponding to Japanese main holidays. The price is fixed (11500 yen) and you can use it 5 times from the first time you use it, each time for one day. It can be shared between several passengers, for example two persons can use the same ticket for two days and it would last one full day available for one person. During the day it is used, you can board the train as much as you want except for the fastest trains (limited express and Shinkansen). It makes it profitable for tourists coming to Japan during japanese holidays and don't plan to make long trips.
The wikitravel page explaining all details is here : http://wikitravel.org/en/Seishun_18_Ticket
A third option to save money on train tickets is to go to a second hand shop dedicated to transportation tickets. It's maybe the less easy option if you don't speak japanese, mainly because you will hardly find them : it's small, all in japanese, usually near main stations but maybe in a small street "somewhere behind", ... Though, if you can find it and speak a little japanese you may buy tickets with interesting discount there. And by the way, they actually send all kind of tickets. You may find discount ones for movie theater, or amusement park too !!
c) Special trains & others
If you're a train addict or just add some fun to your trip you can try one of the following special trains ...
The Nihonkai Express
This is a overnight train linking Osaka to Aomori for a trip of 1023km and 14h47mn along the west coast of Japan. It will cost you 21740 yen for a standard car.
The Wikipedia page about it is here.
The Tsukuba Exress Train
This is an automated high tech train linking Akihabara to Tsukuba. You can even access internet through wireless connection or play with your nintendo ds thanks to the nintendo spot inside the train.
Its english webpage is here.
http://video.alpslab.jp/
This webpage contains videos of roads passed by various means of transportation, and among them trains of course. If you're such curious you want to see the landscape from the driver seat for your train trip, you will find it here.
のりもの勝席ガイド (norimono no kachiseki gaido)
This is a guide describing the smallest details of transportation means, including trains. You will discover there the interior of the trains before boarding them. Only for trains otaku reading japanese ! If you read japanese you can also have a look at this page, describing all the japanese trains and containing a lot of information about JR : http://www.jr-odekake.net/train/category/train.html
Linimo train
This is a magnetic levitation train built for the Expo 2005 and now used to link Fujigaoka station to Yakusa station near Nagoya City. The Wikipedia page is here.
Cable cars
That's not exactly a train but ... In this mountainous country there is of course a lot of them. Some are really impressive. I personally recommend the one of the Mount Koya.
Thomas train
Near the mount Fuji there is one local train with the shape of the main character of the anime "Thomas".
And surely a lot of others funny ones I don't know yet ...
Enjoy your train trip in Japan !!!
What's written below is focused on Kansai area (Osaka, Kyoto, Nara, Kobe, ...) but in general should stay valid elsewhere in Japan (I hope !). If you see mistakes or things to add, feel free to leave a comment to enhance/correct this article !
1) First Step : Find how to go from A to B ?
When I look for my way I always use the wonderful Hyperdia website. It finds itinerary between two stations and describes fees, delay, eventual transfers and time to wait, name of the train line (private companies are included), maps and others useful informations. It even finds itinerary using other means than train if necessary (foot, boat, bus, ...). That's definitely the Bible for Japan transportations itinerary and time schedule !
There, take good care at the line name. In Japan there is not only the national railroad company Japan Rail, but a lot of local private companies (Hankyu, Keihan, Hanshin, etc...). Depending on the place you go you will use one or the other, so keep in mind the name of the station AND the name of the line to avoid confusion. Some stations have the same name but are at different places depending on the company, some others have different names depending on the company but are at the same place. Moreover different cities often have the same name. Be careful when you select departure and destination location !
Lets have a look at screenshots.
This is the main page. On the left side you can enter your starting point and ending point. On the right side, up to three locations to pass through on the way. Enter the name of places in alphabet pronouciation (eg. Osaka, Kyoto, Oshamambe, Otsu, ... not Oosaka, Kyouto, Oshyamanbe, Ootu, ...). Some places may have several writing accepted, like "Kansai Airport" or "Kansaikuko" (kuko means airport in japanese). Then click on "search".
If the name of destination (or departure) you entered can't be found you will see this message. Just come back to the previous page and check for the writing of the name of departure and destination.
If everything goes right you will arrive on this page. On the first line you can choose the date of departure or arrival or "around (what time you want to travel)". The second, third and fourth lines shows your departure and destination. If several places has the same name you can select which one in a list has shown below :
On the fifth line you find : how many answers you want to display (if you've chosen "departure" on the first line it's the X trains departing from the time selected, if it was "arrival" it's the X trains arriving before the time selected); the type of seat you want (reserved or not, ...); the type of transportation you want/don't want to use.
Once everything is as you wish you can click on the "start" button.
Then the list of matching itinerary is displayed. You have a brief summary on the top of the page and you can click on each line to reach directly the corresponding itinerary detailed lower.
For a simple itinerary it looks like the screen shot above. You have first the time required, the distance in kilometer and the fare. Following, the detail of the itinerary with time, name of station, name of line, cost of each section. If you click on the icon in the timetable column in front of a station name you will display the timetable of all the train stopping at this station on the selected day. If you click on the one in front of a line name, you will display the timetable of all the train running on this line for the selected section. You can also find there the number of each train, the detail of distance between stations, boarding platform number, each served stations and time it stops at. On both timetable your train is highlighted to make it easy to find it. If you click on the icon in the information column you will have the detail of the journey for the selected train : train number, detailed distances, stops, stops delay, platform number at each station. In the following columns you can find a links toward reservation tools for trains or planes requiring a reservation (like Shinkansen), link toward car renting services and hostel booking engine, and link toward a map.
If your itinerary is a little bit more complex with several changes and transportation means it's just the same but a little bit longer :
In the first column you also have the transfer time between two trains. Don't forget to check it to be sure you have enough time to change platform with your big backpack ! ;-)
2) Second step : Buy your ticket and enter the station !
Ok now you've found your way and you went at the station.
First case : you are a happy Japan Rail Pass holder.
Sky is blue, sun's shining, birds' singing for you in the trees and your life is a paradise. Just show your pass at the employee near the gate and enter the station.
And don't forget : you have to buy your Japan Rail Pass BEFORE you enter Japan, in your own country. You CAN'T buy it once you're here !!
Second case : any cases different from the first one.
You're an adventurer, you want to fight with the frightening 'salalyman', to have your unknown neighbour sleeping on your shoulder, get crushed on the window by a smily white gloved employee, attacked by a old woman, and wonder why the hell all passengers suddenly get off from you train to immediately get into the one waiting on the other side of the platform while both appears bounded for the same journey... you're a real backpacker ! ;-)
This adventure starts at the gate with the question : how do I buy my ticket ?
You may be scared by the board of the vending machine and choose the counter. In this case printing the page of your journey found on Hyperdia would be a good idea unless you speak a little bit of japanese.
If you prefer the vending machine, actually it's not so difficult except for the Shinkansen. But in Shinkansen station there will always be someone speaking few words of english to help you anyway. The basic way to buy using the machine is :
1) find the cost of your journey on the big board above your head (once again checking for that before with Hyperdia would be helpful). This is the number written below the name of your destination station (the name of main stations is also written in alphabet). The cost is based on the distance between your departure and your arrival, with no consideration for distance really covered. Some people enjoy a trip around big cities having a loop line for the cheapest cost of one station to the following one on the opposite direction. You can even make the whole loop several time if you really love it !
2) insert coins or bills in the machine until you reach the amount required. Machines always give the change and accept bills, but not credit cards ! Buttons with different amounts light up, press the one with the right amount and take your ticket and your change.
That's simple, isn't it ? And even if you mistook the cost of your journey, don't worry. When you will exit at destination, the employee at the gate will help you to regularize your situation and you won't be charge for penalty.
On this typical machine you can see : a bunch of little black buttons, they will light up showing selectable fares as one goes along you insert money; at the left of these buttons small white ones to select how many passengers; down in the middle the hole to insert bills and immediately at its right the hole for the coins; at the bottom the repository for ticket and your change.
Once you've got the ticket, insert it in the gate. If you've got several (it might be the case if you use the Shinkansen for example), insert them all at the same time and don't try to understand the meaning of each one, even after several years here I'm still not sure to have understood ! They/It will get out at the other side of the gate and gate will open. Don't forget to take them back !!! You will need them at the exit. And don't worry if it gets out less tickets than you entered ! At least there must be one, or it means the machine was hungry and you will have to call an employee to help you...
Oh, about the 'gate', if you're used to 2 meters of heavily aggressive and high secured steel doors like in Paris subway, please try to don't laugh loudly at japanese cute plastic saloon gates of 30 cm height ... ;-) Neither try to jump over them or pass without inserting your ticket if there is no door !!!
3) Third step : which train to board in ?
Yatta ! You're inside the station ! Now you have to find your platform number by looking at the electronic board.
If it's written in japanese just wait a little, english translation follows japanese announces. If you are in a smaller station with a mechanical board, names of main stations are also written in alphabet. That's generally enough to find your way. But here comes the beginning of your troubles...
If you use the Shinkansen, in case you have the Japan Rail Pass just take care that you cannot use the Nozomi Shinkansen. Except that, you can board any Shinkansen you wish. If you have a normal ticket, check at the name of your Shinkasen (Hikari, Nozomi, Kodama, ...) and the departure hour and you will find the platform number.
If you use a normal train, you will probably see that several ones depart for your journey. Thinking the earliest the best maybe a mistake. Firstly because you may loose a lot of time. Secondly because you may board on a train that doesn't stop at your station !
The reason is that in Japan transport facilities are wonderfully optimized. For the same journey it exists several types of train stopping at more or less numerous stations between departure and arrival. For example :
普通 (futsuu) : local, stops at every station
準急 (junkyuu) : semi express, stops at 3/4 of the stations
快速 (kaisoku) : rapid express, stops at half the stations
特急 (tokkyuu) : limited express, stops at main stations only
通勤特急 (tsuukin tokkyuu) : special limited express, stops at some main stations only
This is trains types of the Hankyu line between Kyoto and Osaka, which is a heavy loaded traffic line. That's why there is a lot of types of trains. However on small lines you will probably have to choose only between futsuu and something like kaisoku or tokkyuu types, or even futsuu only I think.
All these lines are connected at key stations and trains are synchronized to give you the possibility of optimizing your journey by going quickly to the next key station with a tokkyu train and then change to reach your station with a futsuu train, without loosing time on connection. In some case it's even faster to pass your station a little and come back with a slower train. Now you understand what are doing these Japaneses who change suddenly from a train to another. It's quite a sport to master the best combination if you commute everyday and have others considerations like unbearably crowded special limited express and time you want to stay in your beloved futon ! But for a tourist it probably looks more like a game I think ;-)
By the way, being a tourist with a quite flexible schedule won't save you with certitude from crowded train. Rush hours are quite large so you won't be safe by avoiding train around 8:00 and 17:00 only. You should better consider intervals from 7:00 to 9:00 in the morning, and in the evening it starts at 17:00 and at 22:00 there is still no more places to seat if you travel between Osaka and Kyoto ! So if you want to be sure to have seat, the only solution is to take your time on a slow 'futsuu' and enjoy the landscape ...
On each platform you will find timetable of trains stopping on this platform. Each line corresponds to one hour, the numbers on the lines show the minute the train will stop at the station you are, the color refer to the type of train (look at the bottom to see which color is affected to which train and stations desserved by it), the little symbols indicate the correspondence between two different types of trains on the same line.
4) Fourth step : board the train
May look trivial but ...
On the Shinkansen, there is three kinds of cars : the green car, the reserved seat car, the unreserved seat car. The green car is higher quality of service and of course higher price. The Japan rail pass comes in both type, take care for that. The standard japan rail pass allows you to board in unreserved seat only but of course you can pay a supplement to reserve you seat. If you don't have japan rail pass, I recommend you to don't take a reserved seat. You will save money and it seems to me you will ever be able to have a seat except on some very special periods like Obon or Golden Week.
The type of car is written on it, near the door. Also, you can find a board on the platform, or thanks to electronic display, detailing the car numbers for each type. then just look at the floor and you will find the number of the car you're in front of. If the Shinkansen is not yet here, the location of doors is shown by lines (or symbols) along which you're supposed to queue properly (please !).
On a normal train, you can board almost any car but some have particularities. First, look at the marks on the floor, and do as explained for the Shinkasen. Then check for an important things : if you're the only male in the queue, you're probably attempting to board a "female only car", look at the floor and if you see a sign like the one below you'd better change of queue or a old Japanese lady may try to get you out with her umbrella !!
The point is that this kind of restricted car is not always 'active', for example it can be only during rush hours. But the sign is always here anyway. So if you can't read japanese, to be sure, check for Japanese males in the queue, or change to the next car.
Some cars are also 'non cellular phones' car, where you can't use your phone, but as tourist I doubt you've got one and that's surely why it's not written anywhere in english and you can't understood except if you speak japanese and listen at the conductor instructions. On the Hankyu trains it's the last and the first car, but I don't now about others companies.
5) Fifth step : inside the train
There is several type of trains of course, with various arrangement for seats or electronical equipments.
For the one with long seats on each sides you have to take care that they can be fold back on heavy loaded line to open more space and 'charge' more people in the car. As it folds as a whole take care to don't stay the only one seated bothering all the other wanting to fold it up !
The seats oriented in the sens of march also have a trap. Japanese people hate to seat facing the rear of the train (why ?????), thus train company installed automatic seats (on some train, manual on the others) that change direction automatically when the train stops at terminus and go back from where it comes. If you think like Japanese (and at least one French) "train=bed" don't forget to wake up at terminus. The seat won't care if you're still on it and you may have a violent wake up !!
Except that nothing to fear. I would just recommend to avoid crowded train, really not enjoyable, but that's the same everywhere. By the way there is some advices in this situation. Get as much as possible away from the door, that's where you will have a chance to be able to breath ! If you can't seat just stand in front of a lucky seated guy and pray for him to get off at next station, then jump on the freed 30cm of seat while forgetting all rules of politeness toward the old lady beside you. Crowded train is a wargame !
Speaking about politeness, some cute pictures on the wall try to suggest to passengers the polite way to act inside train. Don't read newspaper, don't listen music, put your bag on your knees or between your legs, don't speak, don't use your phone nor your DS Lite, don't make up, ... In a short shot, be a statue, and please a tiny one ! But after one minute you will start to see the myth of the ultra polite and disciplined Japanese starting to collapse. Take it the peaceful way and try to give a good image of foreigners. Instead, enjoy the noisy but funny grand'ma, the unbelievable make up of boys and miniskirts of girls, the sleeping Japaneses falling in indescribable position or using their unknown neighbor as a pillow, or the completely drunk salary man going back home.
6) Sixth step : When to get off ?
During your journey you will hear the conductor speaking with no break. He's telling the name of next stations, connections, rules described above and so on. Even if you can't speak japanese you may be able to catch the name of the station which is clearly repeated when the train stops. If not you can still understand where you are thanks to the name of each stations written on the pillar of the platform in alphabet. In recent trains digital screens have been installed inside each cars and display (between two advertisements) next stations. In this case it's really easy to understand. Also, description of the line is displayed on top of the doors. But you have to know on which type of train you are (explained in 3) ) to read it.
If you miss your stop, don't worry you can get off at the next one and take another train in the opposite direction. Usually both side of the line are connected without having to pass through the gates so you won't have to pay for your mistake (only your starting and arrival points are taken in consideration). But in very small stations you may have to get out of the station to enter again on the opposite side. If so, you will have to pay a supplement because you went to far, and then buy a new ticket to come back ! To avoid that maybe it would be better to wait until the next big station.
7) Seventh step : Get out the station
Enter your ticket in the gate and just pass through. If you lost it or mistook the fare you will be asked (and eventually helped) to regularize your situation thanks to a dedicated machine near the gates or at counter. I even could got back my money once I mistakenly bought a too much expensive ticket.
In front of the gates you will find a lot of useful information like maps of the area, direction for interesting spot in the area, direction for taxi, bus, connection, services, ... Also, in big stations or stations near some place of interest there is almost always a little tourist information center. It maybe very small but the usual old men/woman working there are always extremely helpful. I have great memories of receiving information in fluent french at the foot of Mount Fuji in a so tiny station... !
Board showing direction for exits, transfer points to subway, shinkansen line, toilet, taxi, information center, ...
At last, maybe you want to keep a souvenir of this 'big' adventure ? There is sometime a free for use inking pad in front of the gates. It seems Japaneses love a lot this kind of souvenir !
8) Some others things to know ...
a) Some examples of fare and time
Here comes some examples of journey by train to help you make up your mind about japanese transportation. Fare, frequency and delay are given roughly and without any guarantee. Refer to Hyperdia for detailed and confirmed informations.
By Shinkansen :
Sendai - Tokyo : 2h12mn, 5800 yen without reserved seat, departure every 10mn
Tokyo - Kyoto : 2h20mn, 8000 yen without reserved seat, departure every 10mn
Kyoto - Osaka (ShinOsaka station) : 14mn, 540 yen without reserved seat, departure every 10mn
Osaka (ShinOsaka station) - Hiroshima : 1h27mn, 5500 yen without reserved seat, departure every 10mn
Hiroshima - Fukuoka (Hakata station) : 1h10mn, 5000 yen without reserved seat, departure every 30mn
By normal train :
Tokyo - Mount Fuji (kawaguchiko station) : 2h23mn, 4270 yen, 2 transfers
Tokyo - Kamakura : 1h, 900 yen
Tokyo - Osaka : 9h, 10000yen, 7 transfers
Osaka - Kyoto : 1h, 500 yen
Kyoto - Nara : 1h, 700 yen
Osaka - Kobe : 24mn, 400 yen
Osaka - Himeji : 1h, 1500 yen
Osaka - Hiroshima : 6h, 6000 yen, 3 transfers
Hiroshima - Onomichi : 1h, 1500 yen
Hiroshima - Fukuoka (Hakata station) : 6h, 6000 yen, 4 transfers
b) Discount Ticket
The king of them is of course the Japan Rail Pass. If you want to see a lot of places in Japan on a short period, this is the indispensable solution. This ticket can be bought for one, two, or three weeks. It will never be said enough : take care that it MUST be bought OUTSIDE Japan ! Thanks to it you can use almost all the JR train, as much as you want. The most you use train, the most you save. For example, if you buy a one week JRPass (28300 yen) and schedule a quite typical go and get back from Osaka to Tokyo (14050 yen X 2), it leaves you all the other trips during the week for free ! Easy to make it profitable ...
The official website is here : http://www.japanrailpass.net/eng/en001.html
Another interesting ticket is the 青春18切符 (seishun 18 kippu). It's a special ticket sold only during three periods of the year, corresponding to Japanese main holidays. The price is fixed (11500 yen) and you can use it 5 times from the first time you use it, each time for one day. It can be shared between several passengers, for example two persons can use the same ticket for two days and it would last one full day available for one person. During the day it is used, you can board the train as much as you want except for the fastest trains (limited express and Shinkansen). It makes it profitable for tourists coming to Japan during japanese holidays and don't plan to make long trips.
The wikitravel page explaining all details is here : http://wikitravel.org/en/Seishun_18_Ticket
A third option to save money on train tickets is to go to a second hand shop dedicated to transportation tickets. It's maybe the less easy option if you don't speak japanese, mainly because you will hardly find them : it's small, all in japanese, usually near main stations but maybe in a small street "somewhere behind", ... Though, if you can find it and speak a little japanese you may buy tickets with interesting discount there. And by the way, they actually send all kind of tickets. You may find discount ones for movie theater, or amusement park too !!
c) Special trains & others
If you're a train addict or just add some fun to your trip you can try one of the following special trains ...
The Nihonkai Express
This is a overnight train linking Osaka to Aomori for a trip of 1023km and 14h47mn along the west coast of Japan. It will cost you 21740 yen for a standard car.
The Wikipedia page about it is here.
The Tsukuba Exress Train
This is an automated high tech train linking Akihabara to Tsukuba. You can even access internet through wireless connection or play with your nintendo ds thanks to the nintendo spot inside the train.
Its english webpage is here.
http://video.alpslab.jp/
This webpage contains videos of roads passed by various means of transportation, and among them trains of course. If you're such curious you want to see the landscape from the driver seat for your train trip, you will find it here.
のりもの勝席ガイド (norimono no kachiseki gaido)
This is a guide describing the smallest details of transportation means, including trains. You will discover there the interior of the trains before boarding them. Only for trains otaku reading japanese ! If you read japanese you can also have a look at this page, describing all the japanese trains and containing a lot of information about JR : http://www.jr-odekake.net/train/category/train.html
Linimo train
This is a magnetic levitation train built for the Expo 2005 and now used to link Fujigaoka station to Yakusa station near Nagoya City. The Wikipedia page is here.
Cable cars
That's not exactly a train but ... In this mountainous country there is of course a lot of them. Some are really impressive. I personally recommend the one of the Mount Koya.
Thomas train
Near the mount Fuji there is one local train with the shape of the main character of the anime "Thomas".
And surely a lot of others funny ones I don't know yet ...
Enjoy your train trip in Japan !!!
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