The airline began operations a fleet of two Douglas DC-3s followed by two De Havilland DHC-6 Twin Otter and a Sud Caravelle III in 1980.

[6] The 1996 Burundian Civil War put a lot of pressure on the airline, and transportation of all forms in the country was paralyzed.

In 1999 the East African Community lifted sanctions on Burundi and the airline resumed operations from February 1, 1999.

[7] The airline continued to provide scheduled flights to nearby regional cities, however in spring of 2007, due to technical issues it temporarily suspended operations.

[9] In January 2013 it was reported that the privatisation of Air Burundi had in part been delayed by the carrier's 90% shareholding in SOBUGEA (Société Burundaise de Gestion Aéroportuaire), the country's airport management company.