The following destinations have been served directly from/to Yogyakarta International Airport:
Airlines |
Destinations |
| Batik Air | Jakarta–Soekarno–Hatta, Palangkaraya, Samarinda |
| Citilink | Banjarmasin, Denpasar/Bali, Jakarta–Halim Perdanakusuma, Palembang |
| Garuda Indonesia | Jakarta–Soekarno–Hatta |
| Indonesia AirAsia | Mataram–Lombok |
| Lion Air | Makassar, Medan, Pontianak, Tarakan |