It was in 1958 that the Faculty of Agronomy of the University of the Belgian Congo and Rwanda-Urundi was created. This faculty was transferred to Bujumbura in 1960 and integrated in January 1964, at the same time as the faculties of philosophy, literature and economics, at the official University of Bujumbura (UOB).
 
In 1965, the École normale supérieure was created with the mission of training secondary school teachers. In 1972, the National School of Administration was created to train state officials.
It was in 1973 that the three institutions, UOB, ENS, and ENA, merged to form the University of Burundi. This merger took place gradually. Initially, ENA was integrated into the Faculty of Economics and Administration. It was in 1977 that UOB and ENA merged completely to become the University of Burundi.
In the early 1980s, four other institutions were created: the Institute of Journalism, the Higher Institute of Commerce, and the Higher Institute of Land Use and Planning Technicians.
In 1989, all these institutions were integrated into the University of Burundi. The main objective of this integration was to make better use of the resources allocated to higher education.