In 2001 a Technical Task Force was appointed to set up the University. Because of the insecurity in Gulu at the time, the Team set up a temporary office at Lincoln Flat 4 at Makerere University. The Task Force consisted of Dr. J.H. Pen Mogi Nyeko , Prof. Mary. J.N. Okwakol ,Dr. Stephen Tikodri , and Mr. N. Peter Egwel Odyomo. The office relocated to Gulu in early 2002.

In October 2002 the University opened at the District Farm Institute located on Awich Street in Laroo Division, Gulu Municipality. The University opened with the Faculty of Science Education and Institute Human Resource Development offering following courses;

• Bachelor of Science Education
• Postgraduate Diploma in Education
• Diploma in Computer Science
• Bachelor of Business Administration
• Bachelor of Development Studies
• Postgraduate Diploma in Financial Management
• Diploma in Secretarial and Information Management
• Diploma in Development Studies

Initially, the University was named Gulu University of Agriculture and Environmental Science and was to specialize in agricultural mechanization. However, it was later proposed that the University should widen its scope beyond agricultural mechanization and produce high-level human resource that can effectively participate in solving the social and economic problems of the country. It was then renamed Gulu University.
From 2002 the University steadily increased its intake, faculties, and programmes due to the demand to satisfy practical needs regionally, nationally, and internationally.

The University now has six faculties and two institutes:

• Faculty of Medicine
• Faculty of Agriculture and Environment
• Faculty of Science
• Faculty of Education and Humanities
• Faculty of Business and Development Studies
• Faculty of Law
• Institute of Peace and Strategic Studies
• Institute of Research Graduate Studies