The President of Islamic Republic of Pakistan is the Patron and the Federal Minister for Science and Technology is the Chancellor of the Institute. The CUI functions under the guidance of the Board of Governors (BoG) headed by the Executive Director, Commission on Science and Technology for Sustainable Development in the South (COMSATS).

The Board of Governors has representation from the Ministry of Science and Technology, Ministry of Education and Training, Higher Education Commission (HEC), educational NGOs and distinguished academia.

The principal academic and administrative officer of the Institute is the Rector, who performs his functions in accordance with the general policy guidelines of the CUI, laid down in the Charter and enforced by the Board of Governors.