Kumamoto Airport offers nonstop service to 28 destinations, served by 12 airlines.
| Destination | Code | Country | Distance | Duration | Airlines |
|---|---|---|---|---|---|
| Amakusa | AXJ | Japan | 76 km | 0h 25m | MZ |
| Busan | PUS | Republic of Korea | 314 km | 1h 10m | ZE |
| Osaka | ITM | Japan | 476 km | 1h 15m | JL, MZ, NH |
| Nagoya | NGO | Japan | 594 km | 1h 20m | JH |
| Nagoya | NKM | Japan | 620 km | 1h 20m | JH |
| Seoul | ICN | Republic of Korea | 651 km | 1h 45m | KE, TW |
| Shizuoka | FSZ | Japan | 712 km | 1h 20m | JH |
| Okinawa | OKA | Japan | 797 km | 1h 35m | NH |
| Tokyo | HND | Japan | 875 km | 1h 35m | 6J, JL, NH |
| Tokyo | NRT | Japan | 935 km | 1h 43m | GK |
| Taipei | TPE | Taiwan | 1,271 km | 2h 25m | CI, JX |
| Shalu | RMQ | Taiwan | 1,381 km | 2h 40m | JX |
| Tainan | TNN | Taiwan | 1,514 km | 2h 45m | IT |
| Kaohsiung | KHH | Taiwan | 1,536 km | 2h 50m | CI, IT |