All train fares are based on distance traveled, and can range from 180 yen all the way to 20,000+ yen per person one way if you take a bullet train across the country. If you're planning some long-distance journeys, you should definitely look into obtaining a Japan Rail Pass.
Also, the fare can be divided up into multiple sections. For example, your fare for a bullet train might actually be your base fare (what you would pay on a regular train) plus express fare (for taking a faster train.)
Back in the days, you had to look at a huge map of destinations and figure out what your trip will cost you, then buy a corresponding fare from the ticket machine. Although you can still do that, the easier option is for you to obtain a proxy chip embedded reloadable charge card. In the Tokyo area, Suica and Pasmo are the more common options. These can be obtained from the same ticket machines and costs 2000 yen. Of that, 500 yen is a refundable deposit and the other 1500 yen comes preloaded on your card for your immediate use. So basically, it's free.
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| The future has been around in Japan since 2001. |
Also, you can use your Suica to pay for a cold beverage out of a vending machine or even at some stores like Seven Elevens!
Now of course, if you don't mind waiting in lines, there's usually also a manned ticket office to go to for help.
The other thing that I should mention is that not all trains in Japan are run by the same company. By far the biggest of these companies is JR (Japan Railways). They run most of the trains around Tokyo as well as all the bullet trains. However, there are other companies as well such as Keisei, Odakyu, and Tobu. The Tokyo Subway system is also a different company, I believe. Fortunately, your Suica will work for all of these companies around Tokyo. From what I understand, however, that is not the case around Osaka. So beware what company's line your itinerary wants you to take!

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