The move will affect some 13,500 passengers flying into or out of Munich, Lufthansa said. Inter-continental flights will not be affected, although delays are expected.
It came after pilots' union Cockpit announced it was taking industrial action between 10am and 6pm (0800 to 1600 GMT) on Wednesday.
The airline has been hit by several rounds of industrial action over its plans to change its early retirement policy.
A strike last Friday hit 26,000 passengers as 218 flights had to be cancelled, AFP reported.