Why use the train?
By far the most popular and useful method of travel used in Japan is the train or as its known shinkansen. Using the train is the most cost effective and quickest way of traveling throughout Tokyo. Train stations and train personal are coming into contact with English more frequently then they used to so English signs are common in Tokyo especially at train stations.
Hours of operation
The trains run from 5:00am and 1:00am, but on certain occasions like New years they might run a little longer. Train’s are almost always on time so if you know the train is coming at 10:00 you should be there at 9:55 ready for it.
What you should expect
Unlike what you may be used to at home, trains in Japan are packed, and by packed I mean packed. Use should expect to have zero personal space since you will be most likely get less then 30 centimeters between you and the person beside you. If you want to try and avoid a full capacity train do your best to make sure you get on the train before its the last train of the day. The last train of the day is always the most packed.
Click to enlarge map ( Map credits: http://www.jreast.co.jp/e/routemaps/index.html
Buying tickets
First of depending on what your goal is, seeing Tokyo only seeing other parts of Japan staying longer then two weeks etc, should weight heavily on what type of ticket you want to buy.
One day Tokyo Metro tickets
You can ride all Tokyo metro lines for: adult ¥710, child: ¥360. The tickets can be purchased at vending machines near the station or ticket office’s at the station.
One day Tokyo Metro and Toei Subway lines tickets
You can ride all of Tokyo Metro and Toei Subway lines for a price of: adult: ¥1,000, child: ¥500. Just like the previously stated tickets you can purchase these at vending machines located near the stations or from the station’s ticket office.
The two tickets I just mentioned should able to get you through 95% of Tokyo with no problems at all.
If your planning on staying in Tokyo for longer then one month you can purchase a one month ticket called the Commuter Pass which lets you have unlimited travel on all Tokyo Metro lines. The cost is ¥16,820 for 1 month ¥47,940 for 3 months and ¥90,830 for six month tickets.
Tokyo train schedule
If you are in Tokyo and need the Tokyo train schedule you can check online at hyperdia
Need more information?
For those confused on the train system I would highly recommend looking at the official Japanese Train station site and for those looking for a train transfer guide I would recommend this site.