The airline will cancel 800 flights on September 2nd affecting "130,000 passengers", Lufthansa said in a statement on Thursday.
Pilots called on more than 5,000 pilots to join in the the industrial action affecting the Lufthansa passenger airline and Lufthansa Cargo after pay negotiations with the German airline collapsed.
The strike will begin shortly after midnight on Thursday and lasts all day Friday before ending at midnight.Â
The disruption to the flight plan could lead to further "individual cancellations or delays on Saturday and Sunday", Lufthansa said.
The companies Eurowings and Eurowings Discover are not affected by the strike and are expected to fly as scheduled. Lufthansa flights from non-German departure points will also take place, provided aircraft and crews are already abroad, the company said.
The airline group voiced regret at the union's decision, saying it had put forward a "very good offer" that would raise the pilots' basic wages by €900 a month.
READ ALSO: Pilots from German airline Lufthansa to strike on Friday
Frankfurt airport, which is Lufthansa's main hub, also released a statement.
The airport said: "Due to a planned strike by the Vereinigung Cockpit (VC), representing Lufthansa pilots on Friday, September 2nd, flight disruptions and cancellations are likely to occur at Frankfurt Airport throughout the day."
They urged passengers to check the status of their flight "and to take advantage of available rebooking options before traveling to the airport".

Why are pilots striking?
The pilot union Cockpit is seeking 5.5 percent wage increase by the end of the year, automatic compensation for inflation and an adjustment of its salary grid.
Lufthansa said the entire package sought by the union would raise pilot personnel costs by 40 percent or €900 million.
The union argued however that to avert labour disputes, the airline must "present a significantly improved offer".
"Currently, we are too far apart. In addition to compensating for the loss of real wages, we now need above all a sustainable solution for the
compensation structure in all occupational groups," said Cockpit's negotiator Marcel Gröls.
It comes after a strike by Lufthansa ground crew staff grounded planes and affected travellers in July.
READ ALSO:Â Lufthansa strike causes travel turmoil in Germany
Air passengers in Germany have also had to deal with chaotic conditions this summer as airports and airlines have struggled with staff shortages following the lifting of pandemic restrictions.Â
Meanwhile, with inflation soaring, collective salary bargaining is expected to be tense in the coming months across Europe.
German consumer prices rose by 7.9 percent in the year to August, according to data published Tuesday by the federal statistics agency Destatis.
READ ALSO: What are your rights in Germany if your flight is delayed or cancelled?
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