In order to visit some faraway places like Okinawa or (northern) Hokkaido, but also because the Shinkansen can be very expensive (especially without a rail pass), one sometimes needs or wants to book a domestic flight in Japan. However, whereas trains mostly use fixed pricing, airlines use dynamic pricing. How to secure the best fares?
When can flights be booked?
Tickets go one sale twice a year on a fixed day common to all airlines. For example, tickets for flights from March 27 through October 29, 2016 all went on sale at 9:30am on January 27. The day when tickets go on sale is announced a couple weeks beforehand.
The old system of selling tickets only from two months before departure is however still used on a few minor routes. Also, flights which are not yet on sale on the domestic market can usually be booked as part of an international ticket.
For tourists: flat 10,800 yen per flight with ANA and JAL
The two major carriers All Nippon Airways (ANA) and Japan Airlines (JAL) have a simple fare for foreign visitors: 10,800 yen per flight (plus a couple hundred yen of taxes), on all flights (except some routes, which are even cheaper, see below). They differ on some details, however, which are described below. Note that, on some short or very competitive routes, the regular advance booking fare available to everybody (described below) may be cheaper than that. Both fares require a round-trip or open-jaw international ticket from a foreign country to Japan, with no restriction on the airline (contrary to some earlier offers which required flying into Japan on an airline in the same alliance).
ANA's fare is called "Experience Japan". It can only be booked on the local ANA website for a country other than Japan (usually, but not necessarily, one's country of residence), and must be booked at least three days in advance. The checked baggage allowance is one piece of up to 20kg, as with regular domestic ANA fares. Changes and refunds are not permitted. There is no limit on the number of flights which can be booked. Flights of five regional airlines which codeshare with ANA (Air Do, Ibex, Starflyer, Solaseed Air, and Oriental Air Bridge) are also eligible. Flights between Sapporo and peripheral cities in Hokkaido (Wakkanai, Memanbetsu, Nemuro, Nakashibetsu, Kushiro, Hakodate) are even cheaper, at 5,400 yen.
JAL's fare is called "Japan Explorer", it has its own booking system. The conditions are mostly the same as with ANA's, except that the checked baggage allowance is two pieces of up to 23kg each, as on JAL's international flights. On the other hand, only up to five domestic flights can be booked per international ticket. In addition to flights of JAL itself, only flights of its subsidiaries J-Air and Japan Transocean Air are eligible, and not flights of other JAL group airlines such as Japan Air Commuter. Flights between Sapporo and peripheral cities in Hokkaido, flights to or from the Tohoku region, and flights between Naha and outlying islands in Okinawa are even cheaper; see the website for details.
For everybody: advance booking discounts and budget carriers
Advance booking discounts
Both ANA and JAL offer advance booking discounts, which must be booked on the airline's Japanese website (which is also available in English). The best fares are available by booking up to 75 days before departure, the "second-best" up to 55 days, and likewise up to 45, 28, and 21 days. Even booking just a couple days in advance will give some discount over the full fare, which is only applied for last-minute purchases, or when all discounted seats have sold out.
Flights of the five regional airlines mentioned above can also be booked through ANA. Flights of all JAL group airlines as well as of Fuji Dream Airlines and Amakusa Airlines can be booked through JAL.
There are five carriers which can be considered "budget": Skymark, Jetstar Japan, Peach, Vanilla Air (set to merge into Peach by March 2020), and Spring Japan (website in Japanese only for flights within Japan). They mostly serve Japan's major peripheral cities, such as Sapporo, Fukuoka or Naha, from Tokyo and/or Osaka. They also serve some more minor cities, especially on the islands of Kyushu and Shikoku.
Skymark is a bit of a "premium budget", in particular all its tickets include a 20kg checked baggage allowance, and also it is the only one of the five which flies domestically from Tokyo's more centrally located Haneda airport. (The other four use Narita, with Peach also using Haneda for international flights only.)
As a general rule of thumb, the sticker price for a flight in a low-demand period (middle of the week, not during holidays) is normally about 8,000 yen with Skymark and 5,000 with the others. However, taxes and payment fees can add up to 1,000 yen, and checked baggage fees can exceed 2,000 yen on long routes or with heavy baggage. During high-demand periods, they usually come close to ANA's or JAL's, since then mostly everything can sell out quickly.
All five run frequent sales campaigns (once or twice monthly), during which fares can sink to about 2,000 yen, with the best discounts being again for flights in low-demand periods. Peach is the only one which announces them on its English website, and it also has an English newsletter. Jetstar and Vanilla have a Japanese newsletter, while Skymark and Spring announce them on their Japanese websites only. However, even when discount fares are only announced in Japanese, they can be booked in English.
There's an excellent option - go to any tourist bureau (HIS, JTB, etc.) and order tickets from there. They normally sell packages, such as tickets plus hotel and it is often way less expensive than booking tickets directly. The only issue with this option is that people in these establishments may not speak English.