The overnight blaze burned through the wooden roof of the Celebi Sultan Mehmed Mosque, also known as Bayezid Mosque, in the town of Didymoticho close to the Greek-Turkish border.
The cause was unclear, though the fire had occurred in the midst of renovation work on the building, completed in 1420. It was a cultural monument rather than a functioning mosque.
"Plumes of smoke are still coming from the building...We should have an idea tomorrow about the cause of the fire," a fire brigade spokeswoman said.
The fire service had been called in on Tuesday because renovation workers smelled smoke, but no fire was detected when the brigade arrived, she added.