The University of Ngozi was created on 17 April 1999 and approved on 7 May 1999. At the time, the Burundian education system was experiencing a significant increase in secondary school enrolment and the situation was likely to lead to an impasse if nothing was done at the level of higher education. The creation of the University of Ngozi then supported and relieved the only public university that existed until then in Burundi, and which was already overstaffed (7000 students for 4000 places in 1999).

The objective was to support the development of higher education in a country that at the time had only one student per 1000 inhabitants, a figure well below the already low African average.

It is through its Faculty of Agronomy that the University of Ngozi intervenes in research on agro-biodiversity by producing selected seeds that are distributed to farmers as is the case with FABI at the University of Burundi.