LCCs operate domestic flights in Japan

There are five LCCs operating in Japan, links to their official site and routes are as following.

Peach Aviation

Operating 14 domestic routes, Osaka(KIX)-Sapporo, Osaka(KIX)-Sendai, Osaka(KIX)-Tokyo(NRT), Osaka(KIX)-Matsuyama, Osaka(KIX)-Fukuoka, Osaka(KIX)-Nagasaki, Osaka(KIX)-Miyazaki, Osaka(KIX)-Kagoshima, Osaka(KIX)-Okinawa(Naha), Osaka(KIX)-Ishigaki, Tokyo(NRT)-Sapporo, Tokyo(NRT)-Fukuoka, Tokyo(NRT)-Okinawa(Naha) and Okinawa-Fukuoka.
Flight Schedule

Skymark

Operating 17 domestic routes, Tokyo(HND)-Sapporo, Tokyo(HND)-Kobe, Tokyo(HND)-Fukuoka, Tokyo(HND)-Kagoshima, Tokyo(HND)-Okinawa(Naha), Ibaraki-Sapporo, Ibaraki-Kobe, Ibaraki-Fukuoka, Ibaraki-Okinawa(Naha), Sapporo-Nagoya, Nagoya-Okinawa(Naha), Kobe-Sapporo, Kobe-Okinawa(Naha), Kobe-Nagasaki, Kobe-Kagoshima, Sapporo-Fukuoka and Fukuoka-Okinawa(Naha).

Jetstar

Operating 16 domestic routes, Tokyo(NRT)-Osaka(KIX), Tokyo(NRT)-Sapporo, Tokyo(NRT)-Fukuoka, Tokyo(NRT)-Okinawa(Naha), Tokyo(NRT)-Oita, Tokyo(NRT)-Kagoshima, Tokyo(NRT)-Kumamoto, Tokyo(NRT)-Matsuyama, Tokyo(NRT)-Takamatsu, Osaka(KIX)-Sapporo, Osaka(KIX)-Fukuoka, Osaka(KIX)-Okinawa(Naha), Nagoya-Sapporo, Nagoya-Fukuoka, Nagoya-Okinawa(Naha) and Nagoya-Kagoshima.

Vanilla air

Operating 3 domestic routes, Tokyo(NRT)-Sapporo, Tokyo(NRT)-Okinawa(Naha) and Tokyo(NRT)-Okinawa(Amami).

Spring Japan

Operating 2 domestic routes, Tokyo(NRT)-Saga and Tokyo(NRT)-Hiroshima.