Euskotren timetables are here: www.euskotren.eus/en/tren/schedules
I believe it's line E1 from Bilbao to Amara Donostia (San Sebastian) then line E2 from Amara Donostia to Irun.
As there's a change, you might be more comfortable choosing bus. But I love the clean, new, cheap, easy Euskotren trains.