Until 1963, the college was virtually dependent on Oklahoma State University, both administratively and academically; however, after 1966, when the first Ethiopian dean was appointed, the role of Americans was limited to advisory and technical support. The College became a chartered member of Addis Ababa University (the then Haile Selassie I University), following the contractual termination of Oklahoma State University in 1968. Consequently, it was named Alemaya College of Agriculture. Due to the great need for trained manpower in other areas of study, additional programs that included a diploma program in Home Economics (1967), Science Teachers’ Training Program (1978), and Continuing Education Program (1980) were launched.

A major landmark in the history of the College of Agriculture was the launching of graduate study programs in the 1979/80 academic year. This laid the foundation for advanced academic and research work at the institution. When graduate studies were launched, about 29 students were enrolled to study various fields of agriculture.

Another major landmark in the history of Alemaya College of Agriculture was when it was upgraded to university status on May 27, 1985, followed by the launching of the Faculty of Forestry in 1987. It was then named the Alemaya University of Agriculture that produced qualified manpower in the fields of Animal Sciences, Plant Sciences, Agricultural Economics, Agricultural Engineering, Agricultural Extension and Forestry both at graduate and undergraduate levels. Moreover, in the continuing education program, diploma level training programs were delivered in Accounting and Management, in Dire Dawa and Harar centres.

The university once again went through another phase of transformation during the 1995/96 academic year by launching new programs in the fields of Teacher Education and Health. The opening of the two faculties, namely the Faculty of Education and the Faculty of Health Sciences, further diversified the existing programs and enabled the institution to become a full-fledged university that was renamed Alemaya University (AU).

In the last few years, the University has witnessed tremendous expansion in terms of fields of study. In September 2002, two more faculties, namely Faculty of Law and Faculty of Business and Economics, were opened. Furthermore, the Faculty of Veterinary Medicine and the Faculty of Technology was initiated in 2003 and 2004, respectively to further diversify the training programs of the university. The institution was renamed Haramaya University in February 2006. The University, apart from undergraduate programs, has been highly engaged in the expansion and diversification of graduate programs.