| IATA | ICAO | Name | City | Type |
|---|---|---|---|---|
| AGJ | RORA | Aguni Airport | Aguni | Small Airport Scheduled |
| AXT | RJSK | Akita Airport | Akita | Medium Airport Scheduled |
| AXJ | RJDA | Amakusa Airport | Amakusa | Small Airport Scheduled |
| ASJ | RJKA | Amami Airport | Amami | Medium Airport Scheduled |
| AOJ | RJSA | Aomori Airport | Aomori | Medium Airport Scheduled |
| AKJ | RJEC | Asahikawa Airport | Higashikagura | Medium Airport Scheduled |
| NGO | RJGG | Chubu Centrair International Airport | Tokoname | Large International Airport Scheduled |
| FUJ | RJFE | Fukue Airport | Goto | Medium Airport Scheduled |
| FKJ | RJNF | Fukui Airport | Fukui | Medium Airport |
| FUK | RJFF | Fukuoka Airport | Fukuoka | Large International Airport Scheduled |
| FKS | RJSF | Fukushima Airport | Sukagawa | Medium Airport Scheduled |
| QGU | RJNG | Gifu Airport | Gifu | Medium Airport |
| HAC | RJTH | Hachijojima Airport | Hachijojima | Medium Airport Scheduled |
| HKD | RJCH | Hakodate Airport | Hakodate | Medium Airport Scheduled |
| HTR | RORH | Hateruma Airport | Taketomi | Small Airport |
| HIJ | RJOA | Hiroshima Airport | Hiroshima | Medium Airport Scheduled |
| HIW | RJBH | Hiroshima Heliport | Hiroshima | Heliport |
| IBR | RJAH | Ibaraki Airport / JASDF Hyakuri Air Base | Omitama | Medium Airport Scheduled |
| IEJ | RORE | Iejima Airport | Ie | Medium Airport |
| IKI | RJDB | Iki Airport | Iki | Medium Airport Scheduled |
| IWO | RJAW | Ioto (Iwo Jima) Airbase | Ogasawara | Medium Airport |
| IWK | RJOI | Iwakuni Kintaikyo Airport / Marine Corps Air Station Iwakuni | Iwakuni | Medium Airport Scheduled |
| IWJ | RJOW | Iwami Airport | Masuda | Medium Airport Scheduled |
| HNA | RJSI | Iwate Hanamaki Airport | Hanamaki | Medium Airport Scheduled |
| IZO | RJOC | Izumo Enmusubi Airport | Izumo | Medium Airport Scheduled |
| NJA | RJTA | JMSDF Atsugi Air Base / Naval Air Facility Atsugi | Ayase / Yamato | Medium Airport |
| HHE | RJSH | JMSDF Hachinohe Air Base / Hachinohe Airport | Hachinohe | Medium Airport |
| MUS | RJAM | JMSDF Minami Torishima Air Base | Ogasawara | Small Airport |
| OMJ | RJDU | JMSDF Omura Air Base | Nagasaki | Small Airport |
| DNA | RODN | Kadena Air Base | Okinawa | Large International Airport |
| KOJ | RJFK | Kagoshima Airport | Kagoshima | Large International Airport Scheduled |
| KIX | RJBB | Kansai International Airport | Osaka | Large International Airport Scheduled |
| KJP | ROKR | Kerama Airport | Zamami | Small Airport |
| KKX | RJKI | Kikai Airport | Kikai | Medium Airport Scheduled |
| KTD | RORK | Kitadaito Airport | Kitadaitōjima | Medium Airport Scheduled |
| KKJ | RJFR | Kitakyushu Airport | Kitakyushu | Medium Airport Scheduled |
| UKB | RJBE | Kobe Airport | Kobe | Medium Airport Scheduled |
| KCZ | RJOK | Kochi Ryoma Airport | Nankoku | Medium Airport Scheduled |
| KMQ | RJNK | Komatsu Airport / JASDF Komatsu Air Base | Kanazawa | Medium Airport Scheduled |
| TJH | RJBT | Konotori Tajima Airport | Toyooka | Medium Airport Scheduled |
| KMJ | RJFT | Kumamoto Airport | Kumamoto | Medium Airport Scheduled |
| UEO | ROKJ | Kumejima Airport | Kumejima | Medium Airport Scheduled |
| KUH | RJCK | Kushiro Airport | Kushiro | Medium Airport Scheduled |
| MYJ | RJOM | Matsuyama Airport | Matsuyama | Medium Airport Scheduled |
| MMB | RJCM | Memanbetsu Airport | Ōzora | Medium Airport Scheduled |
| MMD | ROMD | Minamidaito Airport | Minamidaito | Medium Airport Scheduled |
| MSJ | RJSM | Misawa Airport / Misawa Air Base | Misawa | Medium Airport Scheduled |
| MYE | RJTQ | Miyakejima Airport | Miyakejima | Medium Airport Scheduled |
| MMY | ROMY | Miyako Airport | Miyakojima | Medium Airport Scheduled |
| KMI | RJFM | Miyazaki Airport | Miyazaki | Medium Airport Scheduled |