New Yogyakarta International Airport offers nonstop service to 36 destinations, served by 11 airlines.
| Destination | Code | Country | Distance | Duration | Airlines |
|---|---|---|---|---|---|
| Jakarta | CGK | Indonesia | 423 km | 1h 10m | 8B, GA, ID, IN, QG, SJ |
| Denpasar | DPS | Indonesia | 570 km | 1h 25m | GA |
| Praya | LOP | Indonesia | 691 km | 1h 30m | |
| Banjarmasin | BDJ | Indonesia | 717 km | 1h 30m | JT |
| Palangkaraya | PKY | Indonesia | 761 km | 1h 35m | |
| Pangkal Pinang | PGK | Indonesia | 769 km | 1h 30m | |
| Palembang | PLM | Indonesia | 811 km | 1h 35m | QG |
| Pontianak | PNK | Indonesia | 860 km | 1h 50m | |
| Jambi | DJB | Indonesia | 993 km | 1h 45m | |
| Balikpapan | BPN | Indonesia | 1,056 km | 1h 55m | IP, JT, QG |
| Ujung Pandang | UPG | Indonesia | 1,095 km | 1h 55m | JT, QG, SJ |
| Samarinda | AAP | Indonesia | 1,153 km | 2h 0m | |
| Batam | BTH | Indonesia | 1,196 km | 2h 5m | QG |
| Singapore | SIN | Singapore | 1,226 km | 2h 20m | TR |
| Pekanbaru | PKU | Indonesia | 1,330 km | 2h 5m | JT |
| Padang | PDG | Indonesia | 1,340 km | 2h 10m | |
| Kuala Lumpur | KUL | Malaysia | 1,498 km | 2h 30m | AK, MH |
| Kuala Namu | KNO | Indonesia | 1,780 km | 2h 45m | JT |