As a public university, Muni University operates under the general policies of the Ministry of Education and Sports and is regulated by the National Council for Higher Education.
The University is governed by the Universities and Other Tertiary Institutions Act, 2001 (as amended in 2003 and 2006), which provides for a Council, a Senate, a Management and a Student Guild, among other offices and structures.
Leadership

Rt. Rev. Dr. Henry Luke Orombi
Chancellor
Assoc. Prof. Simon Anguma Katrini
Vice Chancellor and Chairperson of Senate
Eng. Joel Aita
Chairperson, University Council
Mr. Moses Kibrai
Vice Chairperson, University Council
Mr. Ambrose Ocen
University Secretary
Mr. Felix A. Opio Okello
Academic Registrar