CUHAS-Bugando, as a Constituent University College of SAUT, became operational in September 2003. It was granted a Certificate of Interim Authority (CIA) on the 28th March 2002 and a Certificate of Provisional Registration (CPR) on 27th March 2003. By 2005 the College was firmly established and accorded full registration status by the Tanzania Commission of Universities (TCU). The Commission at its 53rd meetingapproved a request from SAUT to transform the College to a full-fledged university and granted CUHAS-Bugando a Certificate of Full Registration.
At its inception it was envisaged that it would be organized in faculties, institutes and directorates. In 2009/2010 it decided to go into a school mode and therefore established four schools: The Weill Bugando School of Medicine (which replaces the Faculty of Medicine), A School of Pharmacy, the Archbishop Anthony Mayala School of Nursing, and a School of Public Health. The new Schools had their first intake in the Academic Year 2010/2011.The Institute of Allied Health Sciences was established within the Bugando University of Health Sciences in 2006/2007