Japan's incredibly efficient train system is perhaps one of the most unique parts about the country. That being said, the elaborate network can be a little confusing at first. So here is a quick beginners guide on how to utilize Japan's Trains!
JR Rail Pass
If you're visiting Japan you're eligible to purchase the JR Rail Pass, if you are resident these are unfortunately unavailable to you. This pass grants you unlimited access to JR Trains for the duration of your visit. There is a Rail Pass option for the whole country as well as cheaper options limited to specified regions. Keep in mind this pass only works on JR Lines, so be sure to research which lines run in the cities that you plan to visit.
Different rail companies exist within Japan, such as JR, Tokyo Metro, Odakyu Electric Railway and the Keio Corporation. Its important to remember this because these lines can exist in the same station, but if you are transferring from one company to another you will need to exit the ticket gate once and re-enter through another. Additionally, company specific Rail Passes such as the JR Rail Pass will only work with JR Lines.
Suica and Pasmo Cards (Metro Cards)
That being said you can swipe into any station easily using a Suica or Pasmo card. These can commonly be purchased at certain ticket booths within most stations. They function as chargeable cash cards which allows you to enter any ticket gate simply by touching the card on the specified area. When you exit at your destination, the system will know which station you boarded from and deduct the specified amount. If you have an insufficient balance, no need to worry. There are charging stations for your card both inside and outside the ticket gate. Just keep in mind these charging booths only take cash, so make sure you always have some on you.
The only exception to these cards typically comes from the countryside. If you are in a rural area there is a chance that you will not be able to use these cards and will have to purchase a paper ticket from the station.
Local vs Express Trains
When boarding the train double check to make sure you are on either a "Local" or "Express" train, if you don't see any indicators chances are the line you are on only has a "Local" line. Despite stopping at the same platform, Express trains will skip certain stations while Local trains will stop at every station along the way. So if you're traveling far away, best to take the Express, if you're traveling to a nearby destination the Express may not stop there.
Buying Bullet Trains (Shinkansen) Tickets
You can buy bullet train tickets online through several different vendors, however through personal experience these sites can be a little hard to navigate. You also can buy bullet train tickets in person at the みどりの窓ぐし(Green Window) at certain JR Stations. There are specific bullet train touch-screen kiosks that allow you to buy tickets but sometimes they will not display all available options. Therefore, if you want all of your bullet train options enter the "Green Window" booth and line up to speak to a station attendant. These attendants are very knowledgable about most of Japan's regions so they will most definitely be able to help you!
When All Else Fails
If you're stuck and unsure of what to do go up to a station attendant or a station attendant booth by the ticket gate and the attendants will happily assist you in navigating.