The UNU Council is composed of 24 members who are appointed by the Secretary-General of the United Nations and the Director-General of UNESCO for six-year terms. Council members are chosen with the aim of achieving a geographic and gender balance, as well as in consideration of major academic, scientific, educational and cultural trends. The selection also seeks to realize an appropriate representation of young scholars.

The Rector, who acts as the chief academic and administrative officer of the University, is also a member of the Council. The Secretary-General of the United Nations, Director-General of UNESCO and Executive Director of UNITAR are ex officio Council members.