The institution was founded in 1996 as Thika Institute of Technology. In 2000, the Institute developed into a commercial college offering management and computer training programmes. Later in the year the Ministry of Education, Science and Technology recognized the institute as a full-fledged institution of higher learning and granted it a full registration approval. In 2005 the Institute became the 1st private institution in Kenya to be allowed to train pharmaceutical technologists by the Pharmacy and Poisons Board of the Kenya Ministry of Health.
In 2006 the Commission for Higher Education (CHE) validated and approved the institute’s request for collaboration with JKUAT to offer both diploma and degree programmes. After fulfilling all the requirements, the Commission for Higher Education issued MKU with the authority to establish a full-fledged privately funded university. In 2011, the university was awarded a charter by the government of Kenya, upon the recommendation of the Commission of Higher Education.