Navigating Japan's Train System
The Japan Train system is an extensive one, and a very confusing one for the first-time traveller. Japan’s public transportation system can be a little overwhelming at first, but once you get the hang of it, it’s actually incredibly convenient and easy to use!
The first order of business that most tourists don’t know is that there are two train companies, The Metro and the Japan Rail (JR). The main difference between them is that the Metro is underground and JR is above ground. The great advantage of JR is that you can use the JR Pass which offers a great discount if you're planning to travel throughout Japan. However, if you are only touring in/around Tokyo, the JR Pass isn’t worth it. Instead, cards such as SUICA or PASMO would be more beneficial since it can get you on almost any train/bus in Tokyo without having to buy tickets each time you change railway companies.
There are several branches of the Japan Railways Group depending on the location--for instance, Japan Railways East (JR East) covers Tohoku and Kanto, where Tokyo is. Likewise, JR West does Kansai and JR Kyushu does Kyushu. Finding a JR Station is easy
There are a lot of different types of trains: local, semi-express, express, rapid, and more. I’ve found that knowing the names for the different types of trains isn’t really important. The important thing to know is which type of train stops at which station. Most train stations offer an easy to read map that shows which trains stop at which stations. In general, the local train stops at every station, and typically doesn’t go very far. Semi-Express trains still stop at a majority of the stations, but may skip a few. Express trains stop at even fewer stations than Semi-Express trains, and so on.
Once you find the rail line you are looking for, head through the gates. If you have a ticket, there will be a little slot for you to insert the ticket. The gates will open for you to walk through. On the other side, your ticket will be sticking up at the end. Make sure to grab it again, as you will need it to get out of the gates at your destination station. If you have an IC Card, all you have to do is place your card on top of the IC Card reader and then gates will open, and you’re good to go.