Pilots' union Vereinigung Cockpit (VC) announced on Wednesday that its members at Lufthansa subsidiary Germanwings would strike for 12 hours from midday on Thursday.
"We regret the inconvenience for passengers," VC said in a statement. "We call on Lufthansa to abandon its rigid stance and help resolve the conflict."
In Berlin’s Tegel Airport, around 40 flights have been cancelled.
A statement from the airline said it was hiring planes from other operators and offering passengers coupons for train services.
It said it had sent out 13,000 emails and text messages to passengers to warn them of the industrial action.
Germanwings warned on their website: “There will be considerable disruption and delays to all of Germanwings' operations.”
It asked passengers still hoping to travel to check their flight's status online.
Anyone whose flight has been cancelled can rebook or get their money back.
Pilots have been at odds with Lufthansa since April over their early retirement and pension arrangements.
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