President Erdogan was seen off by Ankara governor Vasip Sahin at Esenboga International Airport.
Erdoğan will be welcomed with an official ceremony by President of Azerbaijan Ilham Aliyev.
Two leaders will attend the inauguration ceremony of Fuzuli International Airport.
The city of Fuzuli was recaptured by Azerbaijan after 28 years of occupation by Armenian forces.
The airport is completed and was used for the first time on September 5 when passenger aircraft Airbus A340-500 of Azerbaijan Airlines and cargo aircraft Boeing 747-400 owned by Silk Way Airlines made successful test flights, landing at the airport.