| IATA | ICAO | Name | City | Type |
|---|---|---|---|---|
| - | CA-0018 | Aishihik Airport | Aishihik | Closed Airport |
| - | CA-0037 | Bear River Airport | Nacho Nyak Dun First Nation | Closed Airport |
| YXQ | CYXQ | Beaver Creek Airport | Beaver Creek | Medium Airport |
| - | CA-0054 | Blow River Airport | Blow River | Closed Airport |
| - | CEK2 | Braeburn Airport | Braeburn | Small Airport |
| YDB | CYDB | Burwash Airport | Burwash Landing | Medium Airport |
| - | CFA4 | Carcross Airport | Carcross | Small Airport |
| - | CA-0798 | Carcross Cutoff Airport | Whitehorse | Small Airport |
| - | CEB7 | Carcross Seaplane Base | Carcross | Seaplane Base |
| - | CA-0796 | Caribou Crossing Trading Post Airport | Carcross | Small Airport |
| - | CEX4 | Carmacks Airport | Carmacks | Small Airport |
| - | CA-0085 | Casino Airport | - | Closed Airport |
| - | CEZ2 | Chapman Lake Airport | Chapman Lake | Small Airport |
| - | CA-0554 | Clarence Lagoon Water Aerodrome | - | Seaplane Base |
| - | CA-0095 | Clinton Creek Airport | Clinton Creek Mine | Closed Airport |
| YDA | CYDA | Dawson City Airport | Dawson City | Medium Airport Scheduled |
| - | CEG7 | Dawson City Seaplane Base | Dawson City | Seaplane Base |
| - | CA-0791 | Discovery Yukon Airport | Koidern | Small Airport |
| ZFA | CZFA | Faro Airport | Faro | Medium Airport |
| - | CFC9 | Faro/Johnson Lake Seaplane Base | - | Seaplane Base |
| - | CFT3 | Finlayson Lake Airport | Finlayson Lake | Small Airport |
| - | CFS3 | Fort Selkirk Airport | Fort Selkirk | Small Airport |
| YHT | CYHT | Haines Junction Airport | Haines Junction | Medium Airport |
| - | CFE8 | Haines Junction/Pine Lake Seaplane Base | - | Seaplane Base |
| - | CA-0155 | Hart River Airport | Tr'ondëk Hwëch'in First Nation | Closed Airport |
| - | CA-1171 | Herschel Island Field | Herschel Island (Yukon Territory) | Small Airport |
| - | CA-0924 | Herschel Island Water Aerodrome | Herschel | Seaplane Base |
| - | CA-0797 | Hootalinqua Ranch Airport | Carcross | Small Airport |
| - | CFT5 | Hyland Airport | Hyland | Small Airport |
| - | CA-0186 | Ketza River Airport | - | Closed Airport |
| - | CA-0790 | Koidern Airport | Koidern | Small Airport |
| - | CA-0196 | Komakuk Beach DEW Line Station | Komakuk Beach | Closed Airport |
| - | CFP6 | La Biche River Airport | La Biche River | Small Airport |
| - | CA-0206 | Liard Construction Airport | Dawson City | Closed Airport |
| - | CA-0208 | Little Salmon Airport | - | Closed Airport |
| - | CA-0209 | Livingstone Airport | - | Closed Airport |
| XMP | CFC4 | Macmillan Pass Airport | Macmillan Pass | Small Airport |
| - | CA-0218 | Magundy Airport | - | Closed Airport |
| - | CA-0220 | Mallard Airport | - | Closed Airport |
| YMA | CYMA | Mayo Airport | Mayo | Medium Airport |
| - | CA-0898 | Mayo Water Aerodrome | Mayo | Seaplane Base |
| - | CFP4 | McQuesten Airport | McQuesten | Small Airport |
| - | CA-0231 | Mile 102 Dempster Highway Airport | - | Closed Airport |
| - | CA-0234 | Mile 203 Dempster Highway Airport | - | Closed Airport |
| - | CMN4 | Minto | - | Small Airport |
| - | CA-0239 | Minto Airport | Minto | Closed Airport |
| - | CML7 | Minto Landing | Minto | Small Airport |
| - | CA-0900 | Minto Water Aerodrome | Minto | Seaplane Base |
| - | CA-0248 | Mount Nansen Airport | - | Closed Airport |
| - | CA-1165 | Mt Logan Airstrip | Unorganized Yukon | Closed Airport |
| - | CA-0269 | Ogilvie Airport | - | Closed Airport |
| - | CFS4 | Ogilvie River Airport | Ogilvie River | Small Airport |
| YOC | CYOC | Old Crow Airport | Old Crow | Small Airport Scheduled |
| - | CA-0917 | Old Crow Water Aerodrome | Old Crow | Closed Airport |
| - | CFQ6 | Pelly Crossing Airport | Pelly Crossing | Small Airport |
| - | CFY5 | Pine Lake | Pine Lake | Small Airport |
| - | CA-0290 | Porcupine Airport | - | Closed Airport |
| XRR | CYDM | Ross River Airport | Ross River | Medium Airport |
| - | CA-1164 | Scandium City Heliport | (Old) Scandium City | Closed Airport |
| - | CA-0338 | Shingle Point DEW Line Station | Shingle Point | Closed Airport |
| - | CA-0552 | Shingle Point Water Aerodrome | Shingle Point | Closed Airport |
| - | CFQ5 | Silver City Airport | Kluane Lake | Small Airport |
| - | CA-0348 | Snag Airport | - | Closed Airport |
| - | CA-0349 | Squanga Lake Airport | Squanga Lake | Closed Airport |
| - | CA-0364 | Stokes Point DEW Line Station | Stokes Point | Closed Airport |
| YZW | CYZW | Teslin Airport | Teslin | Medium Airport |
| - | CEF9 | Tincup Lake Seaplane Base | Tincup Lake | Seaplane Base |
| - | CA-0384 | Tintina (Conwest) Airport | - | Closed Airport |
| - | CFS7 | Twin Creeks Airport | Twin Creeks | Small Airport |
| - | CA-0743 | Upper Stewart River Airport | Nacho Nyak Dun First Nation | Small Airport |
| YQH | CYQH | Watson Lake Airport | Watson Lake | Medium Airport Scheduled |
| - | CEJ9 | Watson Lake Seaplane Base | - | Seaplane Base |
| - | CFP8 | Whitehorse / Cousins Airport | Whitehorse | Small Airport |
| YXY | CYXY | Whitehorse / Erik Nielsen International Airport | Whitehorse | Medium Airport Scheduled |
| - | CEZ5 | Whitehorse Seaplane Base | - | Seaplane Base |
| - | CAJ2 | Wiley Airport | Eagle Plains | Small Airport |
| - | CA-1166 | Yukonia Airstrip | (Old) Yukonia | Closed Airport |