The CPU Board of Trustees's structure and corporation is headed by a chairman and vice-chairman alongside the university president, the vice-president for administration and finance, vice-president for student affairs, and the vice-president for academic affairs (and research). The General Secretary of the Convention of Philippine Baptist Churches sits as an ex-officio member. The CPU Alumni Association, the faculty and staff are likewise represented in the Board. The president of the university's student government, the CPU Republic, sits as a representative of the students.