Travel from Madrid to San Sebastián

The bus and/or train takes 6 hours on average. A flight takes 1 hour 15 min in the air.
From my own situation I would probably fly or visit another city on the way there since I don't like to spend a day on public transportation.

It takes about 4 1/2 hrs to drive from Madrid to San Seb but it would most likely be the least expensive way of getting there and you could could stop in Burgos on the way. The actual flight time is about 1 hr. 15 minutes but you have to get to the airport, go through security and then get from the airport to San Seb.

The direct trains on this route depart from Madrid Chamartín station (note that it's not Puerta de Atocha) at about 8:00 a.m. and again at 16:00 and take 5.5 hours. That means they still get you into San Sebastian in time for Spanish lunch or dinner times, respectively, but you could also carry on your own sandwiches onboard if you're following your own clock. This train timing is not too long for me. (A train route via Burgos also works, if you want to stop there, but each leg is a separate, reserved train ticket.)

Thanks for the info. Our best option looks to be renting a car since we can split the cost and be more flexible. Thanks to all for your helpful replies.

No idea the total length of your trip, but on the way north, consider a stop in Burgos. It’s cathedral is beautiful with the tomb of legendary El Cid and his wife Dona Jimena. The area around the cathedral and Plaza del Cid are nice for walking and very close together. A couple miles outside of Burgos is the Cartuja de Miraflores. It is the resting place of Queen Isabel’s parents, King Juan II and his wife. Entrance was free in 2017, donations appreciated. In Burgos we stayed at ABBA Burgos. Between the GPS and signs, It was easy to find, was a short walk from the cathedral, and it has its own parking garage. It’s breakfast buffet was very nice.

Miraflores holds a stunning painting, the "Annunciation" by Berruguete. It stopped non-religious me in my tracks.