The University of Duhok was founded on 31st of October 1992, following a resolution by the Parliament of the Kurdistan Region to address the increasing demand for higher education in the region. The first colleges to be established in the university were the College of Medicine and the College of Agriculture.  Initially, the Medical College had 48 students while the College of Agriculture had 166.  During the first two years, the two embargos imposed by the UN on Iraq and by the Iraqi Central Government on Kurdistan contributed to the slow paced growth of the University and the poor economic conditions in Kurdistan.  After these hardships had passed, the university found itself in a position to steer towards advancement and fresh growth. It expanded to establish 14 colleges, each with specialized departments. 

By 2010 the UoD had 17 colleges and a Higher Institute of Planning. After applying a reform in the Kurdistan Region in 2010, the structure of the UoD has changed to a Faculty System. Today, the UoD has 9 faculties with 18 schools, more than 9100 undergraduate students and 660 graduate students.

By 2012 the UoD has begin to build the first Portal academic learning system. The University Portal is the central access point to information relevant to students,teachers lectures and interests at UoD.

The University of Duhok is a member of International Association of Universities (IAU), European Association for International Education (EAIE), and Association of Arab Universities (AARU).