The University of Bahri was established in July 2011, as a successor of the University of Juba, following the secession of the Southern Sudan. After the secession of the Southern Sudan in July 2011, the University of Juba was reinstated at its birth place in Juba; while its Khartoum campus was renamed the “University of Bahri”.  The University of Bahri also accommodated faculty members, students, and workers from the other three southern universities (Upper Nile, Bahr-el-Ghazal and Rumbek).  Thus, University of Bahri was founded on solid and deeply rooted academic legacies of relatively old four national universities.  The University of Bahri was founded with the purpose of adjusting the conditions of Sudanese students and employees of the former national southern universities. This in addition to contributing to building a society of knowledge, and allowing Sudanese secondary school students opportunities of admission in compensation for those lost by the departure of national southern universities.

The University of Bahri has taken over some infrastructure and resources owned by the University of Juba at its venue in Khartoum, in addition to over 80% of teaching staff members and assistant cadres formerly employed by national southern universities.

At present, the University of Bahri is composed of 19 colleges and 3 specialized centers serving around 28000 students at undergraduate and graduate levels. The prime objective of the University of Bahri is to provide competent, principled and proactive graduates to meet the dynamic social and economic challenges of the Sudan and to push frontiers of knowledge through quality education and relevant research, which can be attained via improvement of infrastructure, promotion of staff  exchange programs and establishment of collaborative research teams.