Despite its name, the facilities are located in the municipality of Hondarribia, with the runway stretching like a spit of land along the river Bidasoa right on the Spanish–French border.

The airport primarily serves domestic flights, especially to Madrid, and an international service to London City has commenced as of July 2022.

A scheme is in the pipeline to lengthen the runway (2008) in order to meet the requirements established to provide service for larger aircraft.

Preliminary plans are still coming up against strong opposition, which has added to the economic difficulties facing the carriers using the airport, making its future all the more uncertain.

The following airlines operate regular scheduled and charter flights at San Sebastián Airport: