Domestic Flights

Most international flights to Japan serve Tokyo and Osaka, so if you’re heading to Hokkaido or Kyushu (Hokkaido in particular) it might be easier to land in Tokyo then catch a domestic flight. There are dozens of flights each day from Tokyo to Sapporo, for example, and I took one to Hakodate. Most domestic flights leave Tokyo from Haneda’s excellent, and huge, domestic terminals – a short hop on the Tokyo Monorail from the international terminal.
The biggest carriers are JAL and ANA. You can buy either through some of the big English-language online flight booking services, but I found it was far cheaper to buy direct from ANA and pay in yen – I got an advance fare far lower than the full rate being offered elsewhere.
In order to do this ANA does require a Japanese phone number; I use the Hushed app to get a temporary one on my iPhone. Booking an ANA flight direct is a two stage process: first book, then pay – don’t forget to do the latter, obviously. At the end you get a printable boarding pass.
Besides those two airlines, Japan now has some low cost carriers. Peach and Jetstar have English-language websites. Hokkaido is also served by the not particularly cheap Air Do.