The walkout at the airline’s Frankfurt hub is to be staged between 5pm and 11pm local time affecting short-haul and medium-haul flights.
The six hour industrial action by the Cockpit union has been called in a dispute over an early retirement scheme.
The union said more strikes could come at any time after today’s action.
Pilots walked out from Lufthansa’s budget arm Germanwings a week ago, costing the airline more than €10 million.
The pilots, who also carried out a three-day nationwide strike in April over the same issue, want Lufthansa to maintain a 50-year old scheme that allows them to take early retirement at 55 and still receive up to 60% of their pay.
The airline, which had tried to scrap the scheme entirely, wants to increase the average age at which its pilots retire to 61, to reflect longer life expectancies and a recent European Union ruling that allows pilots to stay in the job until the age of 65.
The latest strikes coincide with the end of the summer holiday period in various German states.
Lufthansa said the strike would affect business travellers and those going away for the weekend. It also criticised the timing of the announcement, at after 5pm local time, saying it made it difficult to add more people to its call centres to deal with rebookings.
The airline, which said domestic passengers could transfer their tickets to travel by rail on Deutsche Bahn, said: “Lufthansa regrets any inconvenience to Lufthansa passengers caused by the threatened strike measures by the pilots union and will do its utmost to minimise impact on passengers. Passenger support and service has paramount priority.
Sourced from Travel Weekly