The Verdi union called on ground personnel at Tegel and Schoenefeld airports to stop work between 4am on Monday to 5am on Tuesday in a dispute over pay.
Swiss cancelled 13 flights between Zurich and Berlin on Monday.
Easyjet said it was working to minimise the impact of the strike but that passengers should expect cancellations and significant delays.
Customers will be contacted by SMS or email if their flight is cancelled, said the airline.
AirBerlin flights between the German city and Zurich are also affected.