[3][4] Air Djibouti was set up as Compagnie Territoriale de Transports Aériens de la Cote Française des Somalis in April 1963 (1963-04) by B. Astraud, who had been operating an air ambulance service in Madagascar and believed Djibouti was in condition to support an airline that would help boost the country's economy.

[5][6] Operations commenced in April 1964 (1964-04) with a fleet of a Bristol 170, a De Havilland Dragon Rapide and two Beechcraft Model 18 aircraft, initially serving Dikhil, Obock and Tadjoura.

[7] With a fleet of two DC-9-30s and two Twin Otters, at March 1990 Air Djibouti had Abu Dhabi, Aden, Addis Ababa, Cairo, Dire Dawa, Hargeisa, Jeddah, Nairobi, Paris, Rome and Sana'a as part of the airline's international network, and flew domestically to Obock and Tadjoura.

[10][11] At March 2000, the A310 was deployed on scheduled routes to Addis Ababa, Asmara, Cairo, Dar-es-Salaam, Dubai, Jeddah, Johannesburg, Karachi, Khartoum, Mogadishu, Mombasa, Muscat, Nairobi, Rome and Taiz.

[2] Air Djibouti was set to relaunch service in late 2015 and 2016[needs update] with Chairman Aboubaker Omar Hadi and CEO Mario Fulgoni.

The government wishes to establish the country as a regional logistics and commercial hub for trade in East Africa, and chose to relaunch the airline as part of this plan.