A Germanwings spokeswoman said that out of a total 164 flights scheduled, some 116 were cancelled, impacting 15,000 passengers.
Hardest hit were the airports Cologne-Bonn and Stuttgart, but flights were also cancelled in Berlin-Tegel and Hamburg, the spokeswoman said.
Germanwings pilots are striking between 6:00 am and midday (0400-1000 GMT).
The carrier said that mostly domestic flights would be affected, forcing passengers to take the train instead.
By contrast, flights to and from holiday destinations were going ahead as scheduled.
The pilots’ union Vereinigung Cockpit already grounded thousands of flights of its parent company Lufthansa during three days of strikes in March and April, costing the airline around 60 million euros ($79 million).