The apex body of UGC (the Board) consists of eleven members headed by the Executive Chairman. Office bearers are either nominated by the government or invited to act as ex-officio members. Upon the recommendation of the Ministry of Education, the Council of Ministers nominates the Executive Chairman and the Executive Member Secretary of the commission from academic leaders and eminent professors. The secretaries of the Ministry of Education and Ministry of Finance, and a member of National Planning Commission (Social Sector/Education Desk) are the ex-officio members. Among the two Vice-Chancellors represented, one is usually from Tribhuvan University and the other from a different university within Nepal. Two distinguished professors and two prominent educationists are nominated to be members of the apex body. The tenure of the members, including the Chairman and the Secretary, is four years from the date of appointment; however, they are eligible to be reappointed. In order to carry out its duties and responsibilities.

The University Grants Commission (UGC) operates with distinct Divisions, Secretariat, Sections, and Units as follows:

Furthermore, UGC occasionally establishes various committees and task force units to fulfill specific responsibilities. As stipulated by the University Grants Commission Act, these committees are authorized for recruitment, university coordination, academic matters, research, quality assurance, and accreditation. The committees include:

Additionally UGC has formed several other teams and special task committees, such as the Reform Committee, Cluster Committee, Peer Review Team, Theme/Task Committee, and University Feasibility Study Task Force. For the purpose of maintaining a systematic archive of its activities and achievements, UGC has established a publication board, which publishes historically significant documents, research articles, articles on current affairs, and annual reports