The pilots' union Cockpit called on its members to stop work between 2301 GMT on Tuesday and 2259 GMT on Wednesday in a long-running dispute over early retirement provisions.
"Despite the strike, the Lufthansa group will be able to operate most of its around 3,000 daily services and offer most passengers alternatives on other flights," Lufthansa said.
"Overall, the airlines of the Lufthansa group will be able to operate around two thirds of its timetabled flights."
Cockpit staged a long series of walkouts last year over management plans to change the pilots' transitional pension arrangements.
Currently, pilots can retire at 55 and receive up to 60 percent of their pay until they reach the statutory retirement age of 65.
Lufthansa wants to scrap the arrangement.