| VA | From | Airport | To | Destination | Type | Distance miles | Frequency | Competitors | |
|---|---|---|---|---|---|---|---|---|---|
| AAA | WAJJ | Jayapura - Sentani | YSSY | Sydney - Kingsford Smith Intl | Medium | 1975.0 | 1 | ||
| CIF | WAJJ | Jayapura - Sentani | VIAG | Agra AB | Long | 4025.5 | 1 | ||
| CIF | WAJJ | Jayapura - Sentani | OISS | Shiraz - Shahid Dastghaib Intl | Long | 5367.8 | 1 | ||
| CIF | WAJJ | Jayapura - Sentani | NTTO | Hao I - Hao | Long | 4698.1 | 0 | ||
| CIF | WAJJ | Jayapura - Sentani | NTGJ | Totegegie I - Totegegie | Long | 5041.8 | 0 | ||
| CIF | WAJJ | Jayapura - Sentani | NZDN | Dunedin | Long | 3030.8 | 1 | ||
| CIF | WAJJ | Jayapura - Sentani | NFFN | Nadi Intl | Medium | 2356.1 | 0 | ||
| FAA | WAJJ | Jayapura - Sentani | AYWK | Wewak - Boram | Local | 198.7 | 0 | ||
| FAA | WAJJ | Jayapura - Sentani | WABB | Biak - Frans Kaisiepo | Local | 276.6 | 1 | ||
| KSA | WAJJ | Jayapura - Sentani | PKMJ | Majuro Atoll - Marshall Is Intl | Medium | 1930.6 | 1 | ||
| RSQ | WAJJ | Jayapura - Sentani | EDDH | Hamburg | Long | 6894.0 | 0 | ||
| RSQ | WAJJ | Jayapura - Sentani | EDDG | Munster-Osnabruck | Long | 7013.3 | 1 | ||
| UFA | WAJJ | Jayapura - Sentani | WAPP | Ambon - Pattimura | Regional | 747.3 | 0 | ||
| UFA | WAJJ | Jayapura - Sentani | AYPY | Port Moresby - Jacksons | Regional | 574.4 | 0 |