One of the things I love most about Japan is the subway/train system. It can be a bit confusing at first because there are a number of private companies that own different train lines. But once you actually start to ride the trains, it is very easy to do.
First and foremost, consider whether or not you need a Japan Rail Pass. If you need it, order well in advance from authorized travel agency so that you have it with you before getting to Japan. You can only get the voucher outside of Japan. *And most importantly, once you receive the voucher, place it with your passport, so that you don’t forget it like I did!
Next, download the app: HyperDia. It is available on both Android and Apple. HyperDia is a website that configures train lines and train times, and are usually on time. What you do is enter your starting train station and your desired destination station (station closest to whatever place you want to visit). The app will then configure a couple of routes that you could take along with the times the train will get to the station,the time the train will depart, and approximately how much fare is needed. It will also tell you the total time it will take from your starting point to the end point. Keep in mind that HyperDia is only from station to station, not the exact location/landmark you want to get to.
Travel Tip: Always have Japanese Currency in your possession when you enter the train station. Japan only accepts their currency, the Yen (no credit cards and no foreign cash exchanges) and there is a chance you can get stuck in the station. True Story: My cousin was traveling and ran out of Yen. She was stuck for two hours until some Indonesian travelers were willing to help her exchange US dollars for Yen.
Taking the Train
There will be some train lines that are operated by JR Company. If so, your Japan Rail Pass will work and allow you to ride with no extra charge. As for other lines, which are operated by private companies, you can either have currency on you to purchase a one-way ticket at the station automated ticket machine, or you can obtain a Pasmo or Suica card. You can purchase them at the very same station automated ticket machine. These cards allow you to deposit funds ahead of time so that you can just tap your way through the gate instead of purchasing a ticket. The cost of the fare will be deducted from your card, and each time you tap out of a station, your balance will appear, so you always know how much funds are left on your card. It is very time efficient to get one so that you aren’t standing in line and making sure you purchased enough funds for a one-way ticket.
Travel Tip: Your Suica and Pasmo card can also be used to purchase beverages and food from many vending machines that accept them. I visited a ramen shop and they accept Suica as a form of payment at their automated menu ordering machine.
Taking the Shinkansen (the famous bullet train) and other Reserved/Unreserved Trains
There will be times when you need to purchase a reserved train ticket, especially for long travels, like from Tokyo to Kyoto. Again, if you already have a JR Pass, you have access to a ticket on the reserved cart at no extra cost. Please note, you need to get a ticket from the Shinkansen counter or Train ticket counter. If you don’t have a JR Pass, you can purchase an unreserved ticket for a much cheaper price. One of the downside is that if the train is busy you may not have a seat. This has never happened to me though.
Travel Tip: Once you arrive at Narita Airport, a reserved train ticket is needed to ride the Express train out of the airport. A one-way trip to Tokyo will cost about US$32, and not to mention the train ride back. So budget that a round trip ticket from the airport and back will set you about US$64. If you plan to visit Kyoto and/or Hiroshima, a JR Pass is a must. A one-way ticket from Tokyo to Kyoto set me back about US$118. (At the time of writing this, a JR Pass is US$238 and would cover these ticket fares).