"The debris of the jet and the pilot's body have been recovered," according to a military statement published online yesterday.
"The cause of the accident will be made public after the investigation."
The military had earlier said the pilot took off from an airbase in Merzifon in northern Turkey and last communicated with the base while "on mission in the Amanos mountains" near the Syrian border.
The accident came two days after a twin car bombing killed at least 50 people in the town of Reyhanli, along the Syrian border, which Turkish authorities blame on groups close to the Damascus regime.
The squadron is equipped with American air-ground AGM-88 HARM missiles designed to detect, attack and destroy radar and communication systems, including air defence positions, it added.