The American University of Afghanistan includes in its management team two Vice Presidents: the Chief Academic Officer and the Chief Finance and Administration Officer.

The Chief Academic Officer and Vice President provides leadership for all academic programs as spelled out in the Academic and Curricular Guidance, the Vision and Mission statement, and other planning documents. New university program development is the priority. The Chief Academic Officer assumes co-campus-wide leadership with the Chief Finance and Administration Officer during the President's absence. Staff members are few and the Chief Academic Officer is asked to do things large and small to mount programs that attract resources and students. Academic quality is paramount. Core areas of the Chief Academic Officer’s portfolio of responsibilities include Academic Affairs, Faculty Recruitment and Development, Enrollment Management, Student Affairs, Foundation, and Professional Development Programs.

The Chief Finance and Administration Officer and Vice President heads the Office of Business Affairs and, in that broad capacity, provides leadership and vision to the management of the University’s financial, administrative, and business operations in support of the educational mission. The Chief Finance and Administration Officer reports to the President of the University, as well as providing advice, counsel and information on all financial and administrative matters at the University. The Chief Finance and Administration Officer is authorized to make decisions as required for the smooth operations of the University, including during times when the President is away from the University. The Chief Finance and Administration Officer oversees the functional areas of Finance, Procurement, Facilities Management, Security, Communications, Human Resources, and Information Technology.