| VA | From | Airport | To | Destination | Type | Distance miles | Frequency | Competitors | |
|---|---|---|---|---|---|---|---|---|---|
| ATR | PAJN | Juneau Intl | PAVD | Valdez | Local | 389.6 | 0 | ||
| CFC | PAJN | Juneau Intl | CAB5 | Bronson Creek | Local | 150.7 | 1 | ||
| CFC | PAJN | Juneau Intl | CYZP | Sandspit | Local | 319.8 | 2 | ||
| CFC | PAJN | Juneau Intl | PAYA | Yakutat | Local | 171.8 | 2 | ||
| CFC | PAJN | Juneau Intl | PANC | Stevens Anchorage Intl | Local | 494.2 | 2 | ||
| EVO | PAJN | Juneau Intl | VHHX | Hong Kong Intl (old) | Long | 4890.8 | 0 | ||
| EVO | PAJN | Juneau Intl | EDDF | Frankfurt/Main | Long | 4049.6 | 0 | ||
| EVO | PAJN | Juneau Intl | TNCA | Aruba I - Oranjestad/Reina Beatrix Intl | Long | 3969.2 | 0 | ||
| NAE | PAJN | Juneau Intl | KDEN | Denver Intl | Medium | 1591.4 | 3 | ||
| NAE | PAJN | Juneau Intl | KMWH | Moses Lake - Grant Co Intl | Regional | 864.1 | 1 | ||
| NAE | PAJN | Juneau Intl | PAEI | Fairbanks - Eielson AFB | Regional | 519.6 | 0 | ||
| NAE | PAJN | Juneau Intl | KSEA | Seattle-Tacoma Intl | Regional | 788.1 | 1 | ||
| NAE | PAJN | Juneau Intl | KMIA | Miami Intl | Medium | 2984.8 | 1 | ||
| NAE | PAJN | Juneau Intl | PHNL | Honolulu Intl | Medium | 2441.4 | 1 | ||
| NAE | PAJN | Juneau Intl | CYVR | Vancouver Intl | Regional | 680.2 | 0 | ||
| NAE | PAJN | Juneau Intl | KAMA | Amarillo Intl | Medium | 1901.0 | 0 | ||
| NAE | PAJN | Juneau Intl | KMCO | Orlando Intl | Medium | 2823.6 | 1 | ||
| NAE | PAJN | Juneau Intl | KRIV | Riverside - March ARB | Medium | 1624.6 | 0 | ||
| NAE | PAJN | Juneau Intl | PHTO | Hilo Intl | Medium | 2484.8 | 0 | ||
| NAE | PAJN | Juneau Intl | KSFO | San Francisco Intl | Medium | 1332.3 | 2 | ||
| NSA | PAJN | Juneau Intl | PABE | Bethel | Regional | 834.9 | 1 | ||
| NSA | PAJN | Juneau Intl | PANC | Stevens Anchorage Intl | Local | 494.2 | 0 | ||
| NSA | PAJN | Juneau Intl | KLAX | Los Angeles Intl | Medium | 1601.9 | 0 | ||
| RSQ | PAJN | Juneau Intl | CYVR | Vancouver Intl | Regional | 680.2 | 1 | ||
| RSQ | PAJN | Juneau Intl | PANC | Stevens Anchorage Intl | Local | 494.2 | 0 | ||
| SCA | PAJN | Juneau Intl | CAB5 | Bronson Creek | Local | 150.7 | 0 | ||
| SCA | PAJN | Juneau Intl | PAIN | McKinley Park - McKinley Natl Park | Regional | 524.8 | 0 | ||
| SCA | PAJN | Juneau Intl | PAGY | Skagway | Local | 70.2 | 0 | ||
| SCA | PAJN | Juneau Intl | PANC | Stevens Anchorage Intl | Local | 494.2 | 0 | ||
| SCA | PAJN | Juneau Intl | KLAX | Los Angeles Intl | Medium | 1601.9 | 0 | ||
| SCA | PAJN | Juneau Intl | CYVR | Vancouver Intl | Regional | 680.2 | 0 | ||
| SCA | PAJN | Juneau Intl | KSEA | Seattle-Tacoma Intl | Regional | 788.1 | 1 | ||
| SCA | PAJN | Juneau Intl | KDFW | Dallas-Ft Worth Intl | Medium | 2144.3 | 0 | ||
| SCA | PAJN | Juneau Intl | BIKF | Keflavik | Medium | 2834.2 | 0 | ||
| SCA | PAJN | Juneau Intl | KDEN | Denver Intl | Medium | 1591.4 | 0 | ||
| SCA | PAJN | Juneau Intl | CYYC | Calgary Intl | Regional | 829.2 | 0 | ||
| SCA | PAJN | Juneau Intl | UUDD | Moscow - Domodedovo | Long | 3964.6 | 0 | ||
| SSF | PAJN | Juneau Intl | KMGM | Montgomery Regl | Medium | 2481.5 | 0 | ||
| UFA | PAJN | Juneau Intl | PAYA | Yakutat | Local | 171.8 | 0 | ||
| UFA | PAJN | Juneau Intl | CYXT | Terrace | Local | 306.5 | 6 |