The management, administration and control of the property, revenue and business of the University fall under the auspices of its Board of Governors. The academic governance of the University is undertaken by its Academic Board  established in accordance with HM Government of Gibraltar University of Gibraltar (Academic Board) Regulations 2018.

External oversight of the governance of the University is provided by the Gibraltar Regulatory Authority (GRA), which has been designated as the Gibraltar Authority for Standards in Higher Education and the Gibraltar Higher Education Commission under the Act. The GRA has issued a Memorandum of Regulation, set out in the schedule of the University of Gibraltar (Regulation and Accountability) Regulations 2018, which describes the information it routinely requires from the University in order to discharge its oversight.

The day-to-day management of the University is undertaken by the Executive Team, which comprises the senior operational staff of the University. The Team is also responsible for preparing the Annual Reports and Financial Statements of the University.