Alvia services use the Madrid–León high-speed rail line as far as Valladolid-Campo Grande, and switches to the conventional rail network to serve Vitoria-Gasteiz and San Sebastián before reaching Irun.

The Barcelona Sants to Irun Alvia service uses the Madrid–Barcelona high-speed rail line to Zaragoza-Delicias before switching to conventional tracks to San Sebastián.

The Cercanías San Sebastián commuter rail line also serves the station.

At present, no connection exists to Bilbao by Renfe tracks; however travel between the two cities by the Euskotren Trena metre-gauge network is provided between Matiko station in Bilbao and Donostia-Amara station.

The Basque Y high-speed rail network will connect San Sebastián station to Vitoria-Gasteiz and Bilbao-Abando in 34 and 38 minutes respectively.