The first colleges established at the University of Duhok were the College of Medicine and the College of Agriculture. Initially, the College of Medicine had 48 students, while the College of Agriculture had 166. During the first two years, embargoes imposed by the UN on Iraq and by the Iraqi Central Government on the Kurdistan Region contributed to the slow-paced growth of the University of Duhok and the poor economic conditions in Kurdistan.
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, 22 schools with 50 Departments.
Today, the university is based on six main sites. It is currently in the process of expanding buildings on a unified campus, which already has most of the schools, thus becoming the final face of the University of Duhok.