In 1954, the University was initially established as a Public Health College and Training Centre (PHC & TC), now known as the College of Medicine and Health Sciences. The establishment of the PHC & TC was mainly due to the pressing and enormous health problems that existed in the 1940s and early 1950s. The aim of the Public Health College and Training Centre was to train teams of middle-level health personnel. The institution started with the philosophy of a team approach and community-based teaching of health professionals. Until 1960, the Ministry of Health ran the College.

In 1961, the College joined the then Haileselassie I University, now known as Addis Ababa University, by acting on an internal decree known as the “Charter of Hailesellassie I University.” In 1978, announcements were made for the establishment of a medical faculty in Gondar College of Public Health and Training Centre by a bilateral agreement reached between the Karl Marx University of Germany and Addis Ababa University. It was a landmark in the long history of the College as it was a significant transformation that resulted in the practical establishment of medical education. In 1988, the name “Gondar College of Medical Sciences” was given to Gondar Public Health College and Training Center (GPHC & TC). The training was initially provided by German medical experts. It created an opportunity for the successive training of Ethiopians in Germany to substitute the German specialists to whom the College’s success was entirely attributed. The College detached from Addis Ababa University and became autonomous in 1992.

In 2001, the first new faculty, the Faculty of Management Sciences and Economics (recently renamed as the College of Business and Economics), was opened. In the spring of 2003, the name of the College was changed to Gondar University College. It was at this time that two new faculties, namely, the Faculty of Applied Natural Sciences (now the Faculty of Natural and Computational Sciences) and the Faculty of Social Sciences and the Humanities (now the College of Social Sciences and the Humanities were added. The Faculty of Veterinary Medicine and the then Faculty of Law (now the School of Law) were opened in 2003 and 2005, respectively. Furthermore, one new faculty, namely, the Faculty of Agriculture, and two schools, namely, the School of Technology and the School of Education, were opened in 2009 and started to enroll students in September 2010.