Olympic Airlines says it will cancel 100 flights Wednesday because a union representing most of its employees will join a public sector worker strike.
Most of those affected are domestic services but international flights to destinations including London, Paris and Istanbul will also be hit.
Wednesday's strike was called by Greece's largest labor union, the GSEE. The protest is also set to halt Athens' metro and intercity rail services for 24 hours, and disrupt other public transport.
Olympic unions oppose privatization plans and on Monday staged a protest at Thessaloniki airport, briefly occupying the runway. Officials at the airport in northern Greece said flights were not disrupted.