| Name | Type | IATA | ICAO | City |
|---|---|---|---|---|
| Banaina Airport | Small Airport | NAF | ID-NAF |
Banaina-Borneo Island |
| Binuang Airport | Small Airport | - | WAQG |
Binuang |
| Binuang Airstrip | Small Airport | - | ID-0032 |
Binuang |
| Bunyu Airport | Small Airport | BYQ | WALV |
Bunju Island |
| Datah Dian Airstrip | Small Airport | - | ID-0042 |
Pertamina Oil & Gas Corp. |
| Juwata International Airport / Suharnoko Harbani AFB | Medium Airport Scheduled | TRK | WAQQ |
Tarakan |
| Kurid Airstrip | Small Airport | - | ID-0037 |
Buduk Kabul |
| Long Alango Airstrip | Small Airport | - | ID-0093 |
Long Alango |
| Long Apung Airport | Small Airport Scheduled | LPU | WAQL |
Long Apung-Borneo Island |
| Long Layu Airport | Small Airport | - | WAQU |
Long Layu |
| Long Mawang Airport | Small Airport | - | WRLN |
Long Mawang-Borneo Island |
| Long Pujungan Airstrip | Small Airport | - | WAQV |
Long Pujungan |
| Long Rungan | Small Airport Scheduled | - | ID-0094 |
Long Rungan |
| Long Sule Airstrip | Small Airport | - | WAQW |
Long Pipa |
| Lumbis Airstrip | Small Airport | - | ID-0097 |
Lumbis |
| Mahak Baru Airport | Small Airport | - | WAEA |
Dumu Mahak |
| Malinau Heliport | Heliport | - | ID-0007 |
Malinau-Borneo Island |
| Nain Baru Airstrip | Closed Airport | - | ID-0108 |
Nian Baru |
| Nunukan Airport | Small Airport | NNX | WAQA |
Nunukan-Nunukan Island |
| Robert Atty Bessing | Small Airport Scheduled | LNU | WAQM |
Malinau |
| Tanjung Harapan Airport | Small Airport Scheduled | TJS | WALG |
Tanjung Selor-Borneo Island |
| Yuvai Semaring Airport | Small Airport Scheduled | LBW | WAQJ |
Long Bawan |