This is “the supreme organ of the University, responsible for the overall administration and ensuring the due implementation of the objects and functions of the University.” (IUIU Act). It is composed of seventeen members appointed as follows;
(a) Five persons appointed by the Secretary General of the OIC from among persons who are Muslims of outstanding academic and scientific attainment who are considered to be eminent personalities in the Muslim world irrespective of their nationalities;

(b) Five persons appointed by the government of Uganda;

(c) The Secretary General of the Organisation of Islamic Cooperation; or a Senior Official of the general secretariat appointed by the Secretary General.

(d) The Chairperson of the Permanent Council of the Islamic Solidarity Fund or the Chairperson's representative who shall be a member of the permanent council;

(e) The Chairperson of the Uganda Muslim Supreme Council or the chairperson's representative;

(f) The University Rector who works as secretary to the council;

(g) The Vice Rector responsible for academic matters;

(h) The leader of the university's students' guild.

According to the Act, the IUIU has 16 members of council. Five of these are appointed by the Government of Uganda, and they include the Minister of Education and the Minister of Foreign Affairs in their official capacities, and three persons nominated from among “prominent Ugandan Muslims.” The other members of council are: the OIC Secretary General, the Chairperson of the Permanent Council of the Islamic Solidarity Fund (ISF), the Chairman of the Uganda Muslim Supreme Council, the Guild President, the Rector, the Vice Rector in Charge of Academic Affairs, and five members appointed by the OIC Secretary General. According to the law, government may replace up to two members at any one time every two years.
Functions of the council

Subject to the Islamic University in Uganda Act (1990, cap 103), the Council as the supreme organ of the university is responsible for;
(a) Direction of the administrative, financial, and academic affairs of the university
(b) Laying down general policy guidelines and take all necessary decisions towards the fulfillment of the objectives and functions of the university,
(c) Approve proposals for the creation of departments within faculties and institutes.
(d) Approve university budget proposals.
(e) Adopt rules and regulations governing faculty members submitted by the executive board.
(f) Approve the appointments of Deans and Deputy deans of faculties and Directors and Deputy directors of other campuses.
(g) Approve university fees.
(h) Approve the final accounts of the university submitted by the executive board.
(i) Determine the academic year of the university.
(j) Make proposals to government of Uganda for amending the University act as it may, from time to time,   appear to the council to be necessary.