There are a variety of ways to travel domestically within Japan on special passes or discounts – two of the most well-known are the Japan Rail Pass, which allows unlimited train rides on JR trains, for a set period (e.g. a 3-day pass, or a 7-day pass), including the Shinkansen, but is only available for those on a tourist visa*; and the Seishun kippu (“Youth Ticket”), which is cheaper, available to anyone, and allows unlimited train rides for a limited period, but is only available during certain times of year, and can only be used on local trains.
But, I only recently learned of another very useful option: ANA Experience Japan Fares, which allow you to fly anywhere within Japan for less than US$100 / €100.
These 10,800 yen flights include (near as I can tell) just about any domestic ANA route. It covers more than 34 airports, including not only the major cities (Tokyo, Osaka, Nagoya, Sapporo), but also smaller airports such as Ishigaki, Yamaguchi-Ube, Yonago, Tokushima, even Hachijô-jima. Flights within Hokkaidô are half the price (5400 yen instead of 10,800 yen).
To use this fare, the following conditions must be met:
・Passenger must reside outside of Japan.
・Passenger must hold a passport issued by any country other than Japan, or be a Japanese passport holder with permanent residency outside of Japan.
・Passenger must hold an international ticket/tickets to and from Japan.
As I found these eligibility requirements just slightly vague, I called ANA to ask for clarification on “must reside outside of Japan.” I was told that even foreigners with a zairyû 在留 card (who are thus, legally, if temporarily, “resident” in Japan), e.g. those on a student visa or a “cultural activities” visa, are eligible for this fare. However, the return ticket (leaving Japan, to return to the home country), even if it’s for many months in the future, is required.
Fuller details are available on the ANA website.
*Or certain other particular cases.