Juneau International offers nonstop service to 16 destinations, served by 4 airlines.
| Destination | Code | Country | Distance | Duration | Airlines |
|---|---|---|---|---|---|
| Hoonah | HNH | USA | 56 km | 0h 20m | J5, X4 |
| Gustavus | GST | USA | 65 km | 0h 25m | AS, X4 |
| Tenakee Springs | TKE | USA | 74 km | 0h 30m | J5 |
| Angoon | AGN | USA | 96 km | 0h 35m | J5, X4 |
| Elfin Cove | ELV | USA | 105 km | 0h 35m | J5 |
| Pelican | PEC | USA | 106 km | 0h 45m | J5 |
| Haines | HNS | USA | 112 km | 0h 35m | J5, X4 |
| Skagway | SGY | USA | 129 km | 0h 45m | J5, X4 |
| Sitka | SIT | USA | 153 km | 0h 45m | AS, X4, J5 |
| Kake | KAE | USA | 160 km | 0h 55m | X4, J5 |
| Petersburg | PSG | USA | 199 km | 0h 47m | AS |
| Yakutat | YAK | USA | 319 km | 1h 0m | AS |
| Klawock | KLW | USA | 325 km | 1h 15m | J5, X4 |
| Ketchikan | KTN | USA | 377 km | 1h 4m | AS, X4 |
| Anchorage | ANC | USA | 918 km | 1h 49m | AS |
| Seattle | SEA | USA | 1,464 km | 2h 28m | AS, DL |