Nagasaki offers nonstop service to 11 destinations, served by 9 airlines.
| Destination | Code | Country | Distance | Duration | Airlines |
|---|---|---|---|---|---|
| Iki | IKI | Japan | 93 km | 0h 30m | NH, OC |
| Fukue | FUJ | Japan | 105 km | 0h 30m | NH, OC |
| Tsushima | TSJ | Japan | 161 km | 0h 35m | NH, OC |
| Busan | PUS | Republic of Korea | 266 km | 1h 0m | BX |
| Osaka | KIX | Japan | 521 km | 1h 20m | MM |
| Kobe | UKB | Japan | 527 km | 1h 5m | BC |
| Osaka | ITM | Japan | 551 km | 1h 15m | JL, NH |
| Seoul | ICN | Republic of Korea | 595 km | 1h 40m | KE |
| Nagoya | NGO | Japan | 672 km | 1h 15m | NH |
| Tokyo | HND | Japan | 953 km | 1h 43m | 6J, JL, NH |
| Tokyo | NRT | Japan | 1,013 km | 2h 0m | GK |