Long haul and cargo flights are being cancelled in Thursday's strike, which will end one minute before midnight. Already, half of the airline's long-haul flights have been cancelled.
"The airports in Frankfurt, Munich and Düsseldorf are affected," a spokesperson for Germany's biggest airline said.
Lufthansa's plans to expand into low-cost intercontinental service is said to have heightened tensions between the company and the union representing its pilots.
Alexander Schumann, chief economist from the German Industry and Business Chamber (DIHK), told the Bild newspaper that the strikes are costing the German economy an estimated €25 million.
Its 36-hour strike Monday and Tuesday had caused around 1,400 flights to be scrapped and disrupted services to destinations including London, Dubai, Seoul, Tel Aviv and Buenos Aires.
Thursday's strike will not affect domestic and intra-Europe flights or services operated by Lufthansa's low-cost subsidiary Germanwings.
The industrial unrest has flared up again since talks between the airline and union broke down last Friday.
The fight mainly centres on transitional pension arrangements for the union's roughly 5,400 pilots. They can currently retire at 55 and receive up to 60 percent of their pay until they reach the statutory retirement age of 65.
Lufthansa, which wants to scrap the arrangement, said in October that combined strike action so far this year had cost it about €170 million.
Pilots say they are also concerned about the airline's future strategy, including plans for a long-haul budget subsidiary where present collective bargaining arrangements would not apply.
On Wednesday, Lufthansa's supervisory board approved the strategy of CEO Carsten Spohr, which comes amid tough competition from low-cost carriers such as Ryanair and Easyjet and Gulf-based carriers.
Under the plan, the Group plans to build up its premium Lufthansa services,but also to offer low-cost long-haul services under the Eurowings banner, with a fleet to be expanded with up to seven Airbus A330-200 jets.
Eurowings will offer budget long-haul services from late 2015 in collaboration with SunExpress, a joint-venture with Turkish Airlines, said the statement.
Initial destinations will be in Florida, southern Africa and the Indian Ocean, the airline said.
SEE HERE: Lufthansa's list of cancelled flights