The University is governed by the two principal organs which are the Council and Senate. The Council is the principal policy making organ of the University. It has committees which include the Finance, Planning and Development; Appointments and Human Resource; Students Affairs and Audit Committee. The Senate is responsible for all academic matters including research, outreach and consultancy services. It receives and makes decisions on matters received from school/faculty/institute/directorate/centre boards. The lowest decision making organ in the University is the departmental committee. The University shall strive to strengthen its governance structures for more efficient and effective operations of the University.

The Governing Board is the highest policy making organ for the University and responsible for the management and administration of the University revenues and properties.

The Academic Committee is the principal overall decision making organ in respect of all academic matter of the University. It is responsible to the Governing Board for the control and general regulation of academic work of the University in teaching, research, extension and consultancy within the University and superintendence of education and discipline of students.

MoCU is headed by the Chancellor who is appointed by the President of the United Republic of Tanzania. The main function of the Chancellor is to confer degrees, diplomas, certificates and other awards offered by the University. The Chancellor is assisted by the Vice Chancellor who is the Chief Executive Officer of the University.The Vice Chancellor is assisted by two Deputy Vice Chancellors; one responsible for academic and the other for administrative matters. The Deputy Vice Chancellors are assisted by Deans and Directors while Deans and Directors are assisted by the Heads of departments.

The University also recognizes the functions of the associations and organizations in safeguarding the interests of their members.