Labuan Bajo offers nonstop service to 10 destinations, served by 7 airlines.
| Destination | Code | Country | Distance | Duration | Airlines |
|---|---|---|---|---|---|
| Bajawa | BJW | Indonesia | 127 km | 0h 45m | IW |
| Ende | ENE | Indonesia | 199 km | 0h 55m | IW |
| Maumere | MOF | Indonesia | 259 km | 1h 0m | IW |
| Praya | LOP | Indonesia | 399 km | 1h 20m | IW |
| Kupang | KOE | Indonesia | 454 km | 1h 35m | IW |
| Denpasar | DPS | Indonesia | 520 km | 1h 10m | ID, QZ |
| Surabaya | SUB | Indonesia | 791 km | 1h 30m | |
| Jakarta | CGK | Indonesia | 1,484 km | 2h 20m | GA, ID, QG, QZ |
| Singapore | SIN | Singapore | 2,073 km | 3h 30m | TR |
| Kuala Lumpur | KUL | Malaysia | 2,368 km | 3h 40m | AK |