The Board of Trustees is the highest governing body of the University. It is composed of distinguished men and women from education, business, government, judiciary and the clergy. Past members of the board include incumbent Philippine President Gloria Macapagal-Arroyo, Former President Diosdado P. Macapagal, Former Senator Jose J. Roy, Most Rev. Oscar V. Cruz, Senator Manuel A. Roxas II, among others.

The Board is assisted by the Management Committee tasked to oversee the daily management and operations of the University. Under the supervision of the Management Committee are the deans and heads of different academic and administrative offices.

The University encourages shared leadership and participatory management in its effort to address the growing demands of the academic community.