Uganda Martyrs University started in 1993 with eighty four students in two Faculties. These were the Faculty of Business Administration and Management (BAM) and the Institute of Ethics and Development Studies (IEDS). In 1997, the Faculty of Science was hived off the Faculty of BAM with three Departments namely; the Department of Economics, the Department of Statistics and Mathematics, and the Department of Computer Science. The Faculty of Science was teaching students for the award of a 3-2-2 Bachelors degree which implies that they were offering 3 courses in the first year, two in the second year and two in the final year.
As time went on, there were both horizontal and vertical developments which took place in the Faculty. At a horizontal level, the Faculty set up a Bachelor of Science degree in Economics and Statistics; Statistics and Computer Science; Economics and Mathematics; Mathematics and Computer Science; Economics and Computer Science; Mathematics and Statistics) in 2000-2001. The Department of Computer Science set up a Bachelor of Science in Computer Science and Information Technology in 2004-2005, and a Diploma in Computer Science and Information Technology in 2005-2006. The Department of Mathematics and Statistics set up a Bachelor of Science degree in Financial Mathematics in 2006-2007. At a vertical level, the Department of Computer Science set up a Master of Science degree in Information Systems in 2006-2007 and a Master of Science degree in ICT Management, Policy and Architectural Designs in 2010-2011.
The Department of Economics set up a Master of Science degree in Development Economics in 2008-2009. In 2018, the department of Computer Science and Information Technology launched a new course of Bachelor of Science in Computer Science. Plans are underway to further develop vertically with introduction of PhD degrees if staff and other resources will allow.