Almost all subway, bus, and train tickets in Japan are pro-rated according to the distance that you travel, so you will first need to look at the route maps that are usually prominently placed above the vending machines to figure out (1) where you are, which is usually indicated by a separate color, (2) where you want to go, and (3) how much it costs. You can figure out this last item by looking at the number alongside the station where you wish to go.
Automated vending machines in Japan generally take up to 10,000 bills
and take coins down to 10-yen coins (usually they won't take 5-yen or
1-yen coins). They do NOT take credit cards !!!
Going through the turnstiles
Usually, this is completely straightforward -- put in your ticket, and out it pops out at the other end of the turnstile, like in any other civilized country. Except when you have a Shinkansen (bullet train) ticket (and you don't have a JR pass): in this case, you'll have two separate tickets, one for the basic fare and one for the super-express additional fare (this is for Shinkansen only). In this case, you have to put BOTH tickets through the ticket turnstiles as you go through.
If you have a JR pass, things will work slightly differently. You don't go through the turnstile; instead, just show the JR agent at the booth your JR pass.
Seating on Japanese trains.
Most local and subway trains have no seat assignments. On some express trains (including the Shinkansen), however, there are two types of cars -- one type for assigned seating and the other for unassigned seating. You pay a little extra (usually on the order of 500 or so JPY, but check the guidebooks to be sure) to get the assigned seat. (There are also the first-class cars called "Green Cars.'') Just read the signs carefully to be sure you're on the right type of car.
If you have the JR Pass, you can get an assigned seat at no extra charge, but to do this you have to go to a JR station ticket booth and have an agent issue you the extra seating ticket(s). If you get onto a train with a JR Pass without having gone to a ticket booth, you can take any seat in the unassigned seating area.
How to read the electronic signs at the tracks
Many (though not all) train platforms in Japan will have electronic
signs that tell you information about the next two trains, in order
(the first train gets listed at the top, and the second train will be
listed below). Usually the information given is the scheduled time of
departure, the type (e.g. "Regular" or "Local express" or "Express"),
and the final destination. Sometimes, though not always, parts of this
information is in English, so you should be able to tell whether
you're getting on the right train.
However, even if there is no
English information given, Japanese trains run on time, and they
ALWAYS list the departure time of the next train, so you should be
able to get on the correct train based on just this piece of
information, if nothing else.
Be at the right location, at the right time.
As I said in the above item,
Japanese trains run ON TIME, and they only stop for literally just a
few seconds (unless you're at the initial station), and you're
expected to get on and off
QUICKLY! You'll be very sad to miss your
Shinkansen bullet train when your ticket cost you over 10,000 yen,
Watch out for "Women-only" cars.
If you're traveling during a weekday, and if you're a male, then be aware of the "WOMEN-ONLY" cars on subways and trains, and (obviously) don't get on them. You can usually distinguish these cars by some special colours (white, pink, and other feminine pastel colours) or some other indication. The places where women-only cars stop are also indicated by some distinguishing sign directly on the platform, so be aware of where you're standing.
(These women-only cars were implemented recently in Japan because of women being sexually harassed on ultra-crowded subways during the rush hours.)