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Domestic Scheduled Flights
| Origin | Destination | Carier |
| JNU | ANC Anchorage, AK | Alaska Central Express |
| JNU | KTN Ketchikan, AK | Alaska Central Express |
| JNU | PSG Petersburg, AK | Alaska Central Express |
| JNU | SIT Sitka, AK | Alaska Central Express |
| JNU | WRG Wrangell, AK | Alaska Central Express |
| JNU | AGN Angoon, AK | Alaska Seaplane Service |
| JNU | ELV Elfin Cove, AK | Alaska Seaplane Service |
| JNU | PEC Pelican, AK | Alaska Seaplane Service |
| JNU | TKE Tenakee Springs, AK | Alaska Seaplane Service |
| JNU | CGA Craig, AK | L.A.B. Flying Service, Inc. |
| JNU | EXI Excursion Inlet, AK | L.A.B. Flying Service, Inc. |
| JNU | GST Gustavus, AK | L.A.B. Flying Service, Inc. |
| JNU | HNH Hoonah, AK | L.A.B. Flying Service, Inc. |
| JNU | HNS Haines, AK | L.A.B. Flying Service, Inc. |
| JNU | KAE Kake, AK | L.A.B. Flying Service, Inc. |
| JNU | KTN Ketchikan, AK | L.A.B. Flying Service, Inc. |
| JNU | PSG Petersburg, AK | L.A.B. Flying Service, Inc. |
| JNU | SGY Skagway, AK | L.A.B. Flying Service, Inc. |
| JNU | GST Gustavus, AK | Skagway Air Service |
| JNU | HNS Haines, AK | Skagway Air Service |
| JNU | SGY Skagway, AK | Skagway Air Service |
| JNU | CYM Chatham, AK | Ward Air |
| JNU | FNR Funter Bay, AK | Ward Air |
| JNU | AGN Angoon, AK | Wings Of Alaska |
| JNU | CUW Cube Cove, AK | Wings Of Alaska |
| JNU | GST Gustavus, AK | Wings Of Alaska |
| JNU | HNH Hoonah, AK | Wings Of Alaska |
| JNU | HNS Haines, AK | Wings Of Alaska |
| JNU | SGY Skagway, AK | Wings Of Alaska |
| JNU | TKE Tenakee Springs, AK | Wings Of Alaska |
There is over 30 domestic flights from JNU airport.
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