All commercial flights at San Sebastián Airport operate through the ground floor of its single passenger terminal, where check-in desks and boarding gates are located. The following airlines serve the airport:
- Binter Canarias: Gran Canaria, Tenerife North.
- Iberia (operated by Air Nostrum): Madrid-Barajas.
- Volotea: Málaga, Menorca, Palma de Mallorca, Seville, Valencia.
- Vueling: Barcelona-El Prat.
Data verified with official sources: iberia.com, airnostrum.es, vueling.com, bintercanarias.com, volotea.com.