Ndejje University was first established in 1992 under a different name and ownership. The University acquired its present status in 1995 under the Anglican Diocese of Luweero. It continued operating under this narrow ownership base until 2002 when the ownership base was enlarged to include all the six Church of Uganda Dioceses in the Buganda Region. The university has three campuses, one in Kampala at Plot 151 Balintuma Road and the other two are located on 200acres of land, in a rural setting at Ndejje Hill, Luweero District.
The university currently has an enrolment of approximately 3000 students pursuing various undergraduate and post graduate programmes under the following faculties;Faculty of Arts
Faculty of Basic Sciences and IT
Faculty of Business Administration
Faculty of Education
Faculty of Engineering and Survey
Faculty of Forest Science & Environmental Management
Faculty of Social Sciences