[5] As of January 2015[update], in addition to the Main Campus, Busoga University maintains several other campuses, including the following:[6] Busoga University was founded in 1999, following the issuance of a tertiary institutional license by the Ministry of Education and Sports.

On 23 February 1993, Busoga College Mwiri’s Board of Governors passed a resolution to establish a university on the same hill and requested Busoga Diocesan Council and the House of Bishops to become the foundation body of the anticipated university.

On 19 November 1994, a University Formation Task Force (UFTF) was appointed "to map out the process of establishing BU" and on 21 April 1995, it presented its report to the Bishop.

On 6 May 1995, the Bishop inaugurated BU in the presence of His Royal Highness the Kyabazinga of Busoga, Henry Wako Muloki.

[6] In 2017, its provisional license was revoked by the Uganda National Council for Higher Education, but it was given permission to reapply after two years.