Japan Rail Group, which holds the vast majority of long range routes as well several local metro (usually overground), offers a multitude of passes both for foreigners and locals that, if used right, can give you incredible amonts of savings - as long as you are doing a lot of traveling between towns (inter-city traveling). While also useful for the aforementioned local overground metros, these passes seldom pay for themselves only with local trains - for that, local passes from private companies or pre-paid cards (IC Cards) will either offer you some savings, or the convenience of not requiring to figure prices and pay tickets every trip.
Japan Rail Passes (JR-Passes)
While the JR Passes only cover lines from Japan Rail Group, these are the vast majority of inter-city traveling. For instance, a round-trip between Tokyo and Osaka alone almost pays for a 7 day pass, but staying 7 days in Tokyo would require you riding JR-lines 30 times a day to come close to pay it up.
JR-Passes come in two forms: The main JR-Pass, that is country-wide and should be purchased from outside Japan (you buy a exchange order - as of 2017 you can buy in Japan but it will cost you 10% more), and only once in the country you get the real pass from the exchange order.
The regional JR-Passes work on small regions that are often very touristy on itself: The JR-Kyushu offer passes for Kyushu, The JR-West offer passes to Chugoku and Kanto region, and the JR-East covers most of Kanto and Tohoku, with some passes going as far as Hokaido. Take a look at the map bellow for the coverage areas:
Each JR Regional office have different passes, here is an extensive list of the most commonly used:
JR-Kyushu↗: All Kyushu, Northern Kyushu, Southern Kyushu
JR-West↗: Kansai Area, Kansai WIDE Area, Kansai-Hiroshima, Sanyo-San'in Area, Kansai-Hokuriku, Hokuriku, San'in - Okayama, Hiroshima - Yamaguchi, Okayama - Hiroshima
JR-Shikoku↗: All Shikoku
JR-Central↗: Takayama-Hokuriku, Ise-Kumano-Wakayama, Alpine-Takeyama-Matsumoto, Mt.Fuji-Shizuoka Pass (most passes are a partnership with JR-West)
JR-East↗: Tohoku, Nagano-Niigata, Tokyo Wide, East-South Hokkaido, Hokuriku Arch, Tateyama Kurobe, N'Ex Tokyo RoundTrip
Private rail company passes
There is not one company running the rails. Japan Rail is the largest and responsible for most long-haul lines, but local metros are usually divided in many companies.
In Tokyo, there is Tokyo Metro, Toei Metro, Tokyu Metro and JR-East. Keep in mind JR passes only cover JR lines.
Since the subways and metros are run mostly by other private companies (although there are over-ground metros operated by JR in several cities, most notably Tokyo), these also offer some passes, that are often either for small travel patches they operate, or just for the metros. Some examples of localized travel passes are:
- Tobu Group's Nikko Passes or Kawagoe Passes ↗ (from Tokyo to Nikko and Kawagoe),
- Tokyu Metro passes ↗ (in Tokyo, Yokohama, Odaiba, Kawagoe, Saitama and more.
- Nankai Electric passes for Osaka and Kyoto region ↗, and much more.
- Kintetsu Pass for most Kansai lines ↗(Osaka, Kyoto, Nara, Nagoya, Ise and combinations)
- N'EX Tokyo Round Trip tickets↗ (Offer a round trip to/from Narita Airport to/from any NE'X station on different dates)
- JR Tateyama Kurobe Option↗, is a discount one-way ticket in the Tateyama Kurobe Alpine Route
While usually limited to one day, most metro (or overground-rail) companies offer an unlimited (or quite generous) pass for a low price, here are some:
- Tokyo* All-lines 1 day pass ↗ (includes ALL companies inside the Yamanote loop, and some lines stretching outside using Tokyo metro and Toei metro).
- JR-East* Tokyo Metropolitan (Tokunai pass) ↗ 1 day pass for JR lines only
- Tokyu* Tokyo pass ↗ 1 day for Tokyu lines and connecting Tokyo metro Lines only.
- Tokyo Metro*'s ↗ 1 day pass for Tokyo metro lines only
- The Tokyo+Toei* ↗ passes (up to 3 day passes) for Tokyo metro and Toei metro lines only
- The Toei pass ↗ 1 day for Toei lines (link also lists others including the Tokyo+Toei from the Toei site perspective)
- Osaka city subway pass ↗ day pass
- Kyoto bus pass ↗.
- Hiroshima Electric ↗ 1-day passes (there is a pass only for the streetcar, and one including the ferry)
These passes are often purchased in stations in Japan.
There are a few programs that offer some discounts for select trips. Here are some that are interesting:
- Platt Kodama One-way special↗: Tokyo-Kyoto/Osaka tickets with 30%+ discount (the catch: using the slowest shinkansen, almost twice the time)
- Japanican Tokyo-Kyoto/Osaka discount↗ : offers 15%~30% discount, depends on route (the catch: unreserved seat trains, which is not so bad)
Pre-paid cards (IC Cards)
Pre-pais cards are cards that come with a balance for you to use in most subway lines. While they are not particularly much of a money saver, they offer a big convenience since you can just pass the card on the blockade and go to your destination without worrying about calculating fare or purchasing on every trip. Once the card balance is over, you can easily use any ticket machine to recharge them. While different companies exist in different regions of Japan, nowadays they are pretty much interchangeable and work on all covered areas thanks to negotiations between the companies (so one often chooses the card whose home area is your last visit, since you can only return the card on their own areas). This Japan-Guide page offer a good insight on these Pre paid cards ↗.
Local Metro passes
What to choose?
If you will travel between cities, your best option is to calculate if a JR-Pass (the main or one of the regional ones) will offer you good savings.
For trips in local areas where either there are no JR Lines, or if you don't have or plan having one such Pass, some of the Private Railways Passes might come in handy.
If you don't have any of these passes, you can get an IC Card just for the convenience of it. If you are willing to pay a little extra (or rather, not take the refund for returning the card), you can even keep them as a souvenir.
Japan-guide holds a extensive list of passes ↗. Remember to read the coverage on each: some cover only one company, others only a small region.