Cuper managed to lead the Spanish side to just one victory in their opening 13 Primera Liga games this season.
Cuper told his squad about his exit before training on Tuesday.
Danish legend Michael Laudrup has been linked with the job as Racing Santander boss.
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Who of Europe’s top strikers will move to England this summer?
After a dreadful start to their Bundesliga campaign, Borussia Dortmund appear to have weathered the storm after going five matches without defeat.