Lufthansa said some 98,000 passengers were grounded by the walkout, which flight crew extended to long-haul flights after Wedensday's action affected short-haul services.
The airline has sought to limit the impact of the strike by introducing an emergency timetable.
Some 4,461 flights have been cancelled in the six days of strikes since last Wednesday, according to Lufthansa.
Pilots on Wednesday launched their 15th round of industrial action since the spring of 2014 after a two-day pause on Sunday and Monday that saw talks break down with the management.
The flight crew organisation planned a demonstration at Lufthansa's hub airport at Frankfurt on Wedenessay morning.
The union has not called for the strike to continue till Thursday so far.