Mount Kenya University Main campus is located in Thika, with other campuses in Nairobi, Parklands, Mombasa, Nakuru, Eldoret, Nkubu, Meru, Kakamega and Kisii. The University has study centres in Malindi, Kisumu, Nyeri and Kericho and marketing offices in Garissa, Isiolo and Kitale

MKU has a Management Board (MB), which is responsible for the implementation of the university policies and undertakes the day-to-day management of the University affairs. The MKU Senate is in charge of all academic matters in accordance with the University Charter. The University is ISO 9001:2015 Certified and is a member of Inter-University Council for East Africa, African Association of Universities, and Association of Commonwealth Universities.

MKU has successfully established partnership with like-minded institutions of higher learning around the globe. Currently the University has over 50 partnerships and linkages at local, regional and international levels.