Germany’s national carrier was hit by strikes in April and over the last two weeks.
The strike on Wednesday at Munich Airport will last from 10am to 6pm.
Lufthansa pilots will not fly any departures from the airport, union Vereinigung Cockpit (VC) said. But flights into Munich are also likely to be affected, a union spokesperson told The Local.
The union added it hoped to reach an agreement with Lufthansa over pilots’ pay and pensions by striking.
“Since Lufthansa’s management has until now put forward no realistic compromise we are forced to take these measures,” the union said in a statement on Tuesday, adding they regretted “any inconvenience” to Lufthansa passengers.
A similar strike at Frankfurt Airport on Friday affected 218 flights and 25,000 passengers. Munich Airport is smaller meaning fewer flights should be hit.
A Lufthansa spokesman said they "completely failed to understand" why the pilots were striking again. The strike is set to hit passengers travelling back for the end of the Bavarian summer holidays. Most schools in Bavaria go back on Monday.
A three-day strike over the pension issue in April also grounded 3,800 flights and affected 425,000 passengers.