Frederick University is governed by the Council and the Senate.

The Council is the highest administrative body of the University and it is responsible for all matters that affect the University. The Council considers financial and administrative issues, the University's infrastructure, the overseeing of staff and the approval of recruitments. The Council is chaired by the President and in case of absence, the duties of the President are carried out by the Vice-President.
 
The Senate is the highest academic body in the University and it is responsible for the academic work undertaken in terms of teaching and programs of study as well as the promotion of academic research and any other academic related activity. The Senate is chaired by the Rector who is assisted by Vice-Rectors.

The organizational chart of the University is provided below:

 Frederick University Organizational Chart

Frederick University Council

The Council of the University consists of:

• Four members of renowned ethos and honor appointed by the Founder of the University
• The Rector
• A member of the academic staff at the rank of Professor or Associate Professor, elected by the Teaching Research Faculty
• The Director of Administration and Finance who has no right to vote
• A representative of the Administrative Staff, elected by the body of the Administrative Staff
• A representative of the students, elected by the students

 At present, the University Council comprises the following members:

University Council Permanent Committees

1. Budgetary and Finance Committee
2. Planning and Development Committee
3. Regulations Committee

Frederick University Senate

The Senate of the University consists of:

1. The Rector as President
2. The Vice Rector or Vice Rectors
3. The Deans of the Schools
4. Two representatives of each School elected by the Teaching Research Faculty of the School
5. The Director of Administration and Finance
6. A member of the Special Teaching Staff of each School, elected by the body of Special Teaching Staff
7. A representative of the students of each School, elected by the students of the School

 At present, the University Senate comprises the following members:
   

Senate Permanent Committees

1. International and Public Relations Committee
2. Research Committee
3. Academic and Student Affairs Committee
4. Disciplinary Committee
5. Postgraduate Studies Committee
6. Distance Learning Committee

University Centers

Supplementing the academic and administrative structure, the supreme bodies of the University have the authority to establish Centres. A Centre reports directly to a supreme body and has an executive capacity to engage on a particular area of interest, either within the university of beyond, that spans the scope of several Schools or Services.

• Personal and Professional Development Center at Frederick University (P²DF)
• Center on Gender Issues, Diversity and Equality at Frederick University (ENAF)