Shimojishima Airport offers nonstop service to 16 destinations, served by 3 airlines.
| Destination | Code | Country | Distance | Duration | Airlines |
|---|---|---|---|---|---|
| Okinawa | OKA | Japan | 294 km | 0h 50m | BC |
| Taipei | TPE | Taiwan | 396 km | 1h 10m | JX |
| Shalu | RMQ | Taiwan | 465 km | 1h 18m | JX |
| Fukuoka | FUK | Japan | 1,099 km | 2h 0m | BC |
| Busan | PUS | Republic of Korea | 1,205 km | 2h 15m | LJ |
| Seoul | ICN | Republic of Korea | 1,407 km | 2h 35m | LJ |
| Kobe | UKB | Japan | 1,459 km | 2h 5m | BC |
| Tokyo | HND | Japan | 1,840 km | 2h 35m | BC |