The governance and management structures of the University include The Board of Trustees, The University Council, The University Senate and The University Management Board.

The Chancellor; who is the Titular head of the University, is Professor Emmanuel Tumusiime Mutebile.

The Board of Trustees (BOT)

The Board of Trustees (BOT) is the highest authority of the university and constitutes the proprietors and other appointed members. The overall function of the BOT is to provide overall oversight and strategic direction of all operations of the university. The IUEA University Board of Trustees is chaired by the His Lordship Justice Alphonse Owiny Dollo, other board members are Mr. Alwi Hassan, Ambassador Moses Kiwe Sebunya, Mr. Mohammed Mubiru, Mr. Jack Ogola, Mr. Hassan Alwi Jr ( Resident Director) and Mr. Hassan Alwi Albeity.

The University Council

This is the governing organ of the University and is responsible for the overall administration of the University which includes oversight of administrative, financial and academic affairs. Council makes policies and oversees their implementation by management.

The University Council is chaired by Hon. Hellen Asamo, M.P for People with Disabilities Eastern Region, Dr. Jacinto Amandua, Mr. Dison Okumu, Ms. Leila Namubiru and Mr. Hassan Alwi Jr( Resident Director), Ambassador Moses Kiwe Sebunya, Professor Olubayi Olubayi, who is the Vice-Chancellor and Mr. Amos Olal Odur, who is the acting University Secretary.

The University Senate

This is composed of the Deans of Faculty and senior academic staff. It is chaired by the Vice Chancellor and the Academic Registrar is the Secretary. The senate is responsible for the organization, control and direction of the academic matters of the university. It is in charge of teaching, research and the general standards of education and research and their assessment.

The Management Board

This is the organ responsible for the day-to-day management and running of the University. It is composed of the Vice Chancellor, as the Chairman, and all heads of administrative departments and units as members.