If you're coming to Japan for the first time, one of the first things I recommend doing is picking up a metro map from the airport or a major train station.
Be aware that Tokyo, and Yokohama, have more than one railway company. You have JR (Japan Rail), which operates trains all over the country; they also have lots of stations throughout Tokyo and Kanagawa prefecture. Many cities also have their own subway, like the Yokohama City Subway, and the Tokyo metro. So if you pick up a Tokyo metro map, it may not have all the JR stations on it; likewise, a JR map may not have subway stations on it. Also, if you have a special pass that allows you unlimited use of a particular line - JR or metro or whatever - you probably won't be able to use it on other lines.
How to ride a train
1. Check the map and fare
It shouldn't be too hard. Let's imagine you're at Yokohama station and using JR. You go to the ticket machines and there is a big JR map above them, showing the different stations and the fee for each. (Occasionally at less important stations, this map will be all in kanji, and you're screwed. Hahaha...)
You see that it will cost you 450 yen and that either the Tokaido line or Keihin-Tohoku lines will take you there. The Tokaido line has considerably fewer stops between Yokohama and Tokyo, so it will obviously be faster (though they run less frequently and there may then be less opportunity of getting a seat).
2. Buy a ticket and check the route
Now you know the fare, you can put your 450 yen in the ticket machine and buy a ticket.
If you do not have a map or a clue where you're going, you will want to check the map to see some of the other stations in the direction you want to go. Once you get in the station, it's more difficult to find full railway line maps (though they are inside the trains themselves), and if you're going to a smaller station, it might not be immediately obviously which direction train you should take, since most trains and platforms are labelled with two or three main stations in that direction, eg 'for Kawasaki, Shinagawa, Omiya' or 'for Kannai, Ofuna'.
(If you use trains regularly, you might want to buy a card like Suica or Pasmo. That way, rather than buying a ticket every time you go to a station, you can put credit on the card and swipe it over the card reader on ticket gates. These can also be used in selected vending machines, buses and stores bearing the Suica/Pasmo logos.
If you plan a lot of travel in one day, day pass tickets are also possible.)
3. Go to your platform and check the type of train
Then put the ticket in the ticket gate - take it as you go through - and now you can go to your platform. Check the signs for your platform and destination. Sometimes, as with the Tokaido line, one train line will have more than one platform, and occasionally, one platform may have more than one train line (or lines that change their name after a particular station).
Once you're on the platform, you can find maps of the line you are on. You might have to walk up and down the platform to find one, but they do exist. These maps should also show the route of the local trains (stop at every station), rapid trains (stop at some stations), limited express trains (stop at major stations), etc. This is important as if you're not going to a major station, the rapid/limited express trains may not stop there.
One other point is that some kinds of trains, including some limited express trains, require reserved seating and therefore an extra fee. If this is the case there will usually be a ticket machine on the platform itself. The Tokaido line has regular trains with 'green cars' for those wanting the comfort of a guaranteed seat; these green cars require a reserved seat and extra fee, but you can ride on a regular car for no extra fee.
4. Changing train lines
If you have to change train lines, it's not too difficult. Unless you're changing to a different railway (eg, JR to Keikyu, Yokohama Subway to JR), you shouldn't need a new ticket or to exit through any gates, but can change within the station on the same ticket you originally purchased.
5. Getting out
Once you get out, put your ticket in the machine again, and the machine will eat it.
Incidentally, you can enter a station on the cheapest possible ticket, and then travel anywhere you like. If you've gone further than the price of your ticket - eg, you changed your mind and went further than you expected - the gates won't let you out until you've paid the balance. But you can easily pay on exit. There are 'fare adjustment machines' inside train stations, in which you can top up your ticket (or Suica/Pasmo) so you can get out.
Train times
First trains usually start running at or after 5am. Last trains are often around midnight, maybe as late as 1am. It depends where you're taking it from. A station near the end of the line will obviously have a later 'last train' than one near the beginning. Also, some last trains don't go all the way to the end of the line. And if you're changing trains, you gotta be aware of the time of your last last train! I speak from experience. Taxis are expensive in Japan, and if you get stranded too far from your station, you might end up sleeping in an Internet cafe or doing all-night karaoke (again, I speak from experience ^_^).
In short
I made taking trains sound more complex than it is. Actually, taking trains in Japan is *usually* quite simple, provided you know where you are going and what lines to take. Again, I strongly advise getting a map, or at least checking carefully where you're going before entering the station. And make sure what kind of train you are getting on, whether it's a local or rapid...
Links
You see that it will cost you 450 yen and that either the Tokaido line or Keihin-Tohoku lines will take you there. The Tokaido line has considerably fewer stops between Yokohama and Tokyo, so it will obviously be faster (though they run less frequently and there may then be less opportunity of getting a seat).
2. Buy a ticket and check the route
If you do not have a map or a clue where you're going, you will want to check the map to see some of the other stations in the direction you want to go. Once you get in the station, it's more difficult to find full railway line maps (though they are inside the trains themselves), and if you're going to a smaller station, it might not be immediately obviously which direction train you should take, since most trains and platforms are labelled with two or three main stations in that direction, eg 'for Kawasaki, Shinagawa, Omiya' or 'for Kannai, Ofuna'.
(If you use trains regularly, you might want to buy a card like Suica or Pasmo. That way, rather than buying a ticket every time you go to a station, you can put credit on the card and swipe it over the card reader on ticket gates. These can also be used in selected vending machines, buses and stores bearing the Suica/Pasmo logos.
If you plan a lot of travel in one day, day pass tickets are also possible.)
3. Go to your platform and check the type of train
Then put the ticket in the ticket gate - take it as you go through - and now you can go to your platform. Check the signs for your platform and destination. Sometimes, as with the Tokaido line, one train line will have more than one platform, and occasionally, one platform may have more than one train line (or lines that change their name after a particular station).
Once you're on the platform, you can find maps of the line you are on. You might have to walk up and down the platform to find one, but they do exist. These maps should also show the route of the local trains (stop at every station), rapid trains (stop at some stations), limited express trains (stop at major stations), etc. This is important as if you're not going to a major station, the rapid/limited express trains may not stop there.
One other point is that some kinds of trains, including some limited express trains, require reserved seating and therefore an extra fee. If this is the case there will usually be a ticket machine on the platform itself. The Tokaido line has regular trains with 'green cars' for those wanting the comfort of a guaranteed seat; these green cars require a reserved seat and extra fee, but you can ride on a regular car for no extra fee.
4. Changing train lines
If you have to change train lines, it's not too difficult. Unless you're changing to a different railway (eg, JR to Keikyu, Yokohama Subway to JR), you shouldn't need a new ticket or to exit through any gates, but can change within the station on the same ticket you originally purchased.
5. Getting out
Once you get out, put your ticket in the machine again, and the machine will eat it.
Incidentally, you can enter a station on the cheapest possible ticket, and then travel anywhere you like. If you've gone further than the price of your ticket - eg, you changed your mind and went further than you expected - the gates won't let you out until you've paid the balance. But you can easily pay on exit. There are 'fare adjustment machines' inside train stations, in which you can top up your ticket (or Suica/Pasmo) so you can get out.
Train times
First trains usually start running at or after 5am. Last trains are often around midnight, maybe as late as 1am. It depends where you're taking it from. A station near the end of the line will obviously have a later 'last train' than one near the beginning. Also, some last trains don't go all the way to the end of the line. And if you're changing trains, you gotta be aware of the time of your last last train! I speak from experience. Taxis are expensive in Japan, and if you get stranded too far from your station, you might end up sleeping in an Internet cafe or doing all-night karaoke (again, I speak from experience ^_^).
In short
I made taking trains sound more complex than it is. Actually, taking trains in Japan is *usually* quite simple, provided you know where you are going and what lines to take. Again, I strongly advise getting a map, or at least checking carefully where you're going before entering the station. And make sure what kind of train you are getting on, whether it's a local or rapid...
Links
I've plugged these site a couple of times before, but check out Hyperdia, through which you can plug in any two station names in the country and it will give you the possible routes, cost and travel times between them.
Japan-Guide also has a good section on transportation, for example, Transportation in Tokyo.
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