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Updated: July 12, 2023

A quick overview

Tokyo's public transportation system might be gargantuan and labyrinthine, but it is also efficient, punctual, and excellently maintained. Here's a quick overview: Tokyoites distinguish between the "train" (aboveground trains) and the "subway" (underground trains). Most aboveground trains in central Tokyo are run by JR (which you can ride using your JR Rail Pass, if you have one). The subway system, which also runs primarily in central Tokyo, has two major operators: Tokyo Metro and Toei Subway. Then there are various private train lines that run out through the Greater Tokyo area.
This might sound pretty complicated, but the system works as one seamless whole. In fact, you can access it all with one card.

IC cards (Suica & PASMO)

If you are going to be in Tokyo for even just a few days, and you plan on using public transit, consider a Suica or PASMO IC card. These are rechargeable smart cards that allow you to ride and transfer between virtually all lines in Tokyo. The Suica and PASMO are offered by different companies, but they are more or less the same thing, so don't worry about which one to choose. You can buy one at most train stations for a refundable 500-yen fee. Just charge it with however much money you want, and board your train or bus of choice by tapping it on the ticket gate or stand. When your card runs low on money, just recharge it at the automated ticket machines found at every station. (These machines offer English guidance—look for the "English" button.)
There are also some special IC cards just for short-term visitors to Japan, such as the Welcome Suica, which does not require a deposit, or the PASMO PASSPORT, which comes with discount coupons.

Cheap Tickets & IC Cards

Buying a ticket

If you don't have a smart card, you can of course purchase a paper ticket. Walk up to a ticket machine at the station, look at the fare map, and insert the amount of money you'll need to get to your destination. Most stations will also have an attendant who can help you. If you're transferring between train lines and you pass through a ticket gate, after you insert your ticket, don't forget to collect it on the other side of the gate.

Finding your route

HyperDia and Jorudan are two sites that let you search timetables and routes across Japan. Just type in your start and end stations, and a list of recommended routes will pop up, including notes on which route is fastest, cheapest, and/or most convenient.

Some other pointers

  • Line up to board the train at the designated spots. Don't try to rush past other people as soon as the doors open.
  • Eating or drinking on the train is generally frowned upon, as is talking on your cell phone.
  • Be conscious of your space. If you have a big backpack, turn it around and wear it on your front, or place it between your legs.
  • If you're out late, bear in mind that your last train home will probably be between 23:30 and 00:30 the next day. The first trains of the morning start around 5:00.
  • Trains have priority seats that should be given first to passengers who are pregnant, elderly, or who have disabilities.
  • Many train lines offer women-only carriages during peak hours. These carriages may also be used by elementary-school-aged (or younger) children, as well as people who are physically challenged and their caregivers, even if they are not women.