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 (Vice Chancellor), Prof. Mary. J.N. Okwakol (Deputy Vice Chancellor), Dr. Stephen Tikodri (University Secretary), and Mr Peter Egwelu (Academic Registrar). 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 course:
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 Science;
Diploma in Development Studies.
Gulu University was legally established by a Statutory Instrument No. 31 of 2003. Initially, the University was named Gulu University of Agriculture and Environmental Science and was to specialise in agricultural mechanisation. However, it was later proposed that the University should widen its scope beyond agricultural mechanisation 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.