The airline operates out of Scottish airports including Edinbugh and Glasgow.
The airline said about 400 flights have been cancelled on Thursday, including most connections inside Germany.
Many of its European flights have also been cancelled but long-distance services and those from Frankfurt and Munich are not affected.
The UFO union called the 24-hour strike starting at midnight after arbitration failed to achieve an agreement late on Wednesday.
Members are seeking concessions on issues including pay, working conditions and pensions.
Eurowings, which also operates flights under the Germanwings brand, said customers should check its website to see whether their flight is affected.