The Office of the Vice Chancellor for Academic Affairs (OVCAA) was first organized upon the recognition of the UP Health Sciences Center (UPHSC) as an autonomous component of the UP System through Executive Order No. 519 dated January 24, 1979. 

In 1982, UPHSC was integrated with UP College Manila (the de facto College of Arts and Sciences) and was renamed UP Manila through EO No. 4 issued by the President Edgardo J. Angara. Subsequent reorganizations occurred in 1987 and 1988 which led to the formation of a “Staff Office”  and abolition of the offices of the vice chancellors;  this office was mandated to “provide the Chancellor with manpower for the purpose of conducting studies, preparing development plans for the programs and projects and advising him/her on academic, administrative, fiscal and related matters” with the help of Assistants to the Chancellors.

The Assistant for Academic Affairs supervised and coordinated the Academic Services Offices that included the Office of the Registrar, the Office of Student Affairs, the Office of Research Services, the Office of Graduate and Continuing Education, the Office of Alumni Affairs, and the Office of Information, Publication and Public Affairs. It was a different title but the functions were those of a Vice Chancellor for Academic Affairs.

Through the years, it has become clear that the work of the Assistants to the Chancellor was basically the same as that being performed by Vice Chancellors in the other constituent universities. The Assistants to the Chancellor have progressively assumed the regular functions of Vice Chancellors. They have shared the same responsibilities  and duties assumed by their counterparts. 

At its 1144th meeting on 31 August 2000, the Board of Regents approved the proposal to reinstitute the Offices of Vice Chancellors in UP Manila.

The following have assumed the position of Vice Chancellor for Academic Affairs:

• Dr. Horacio Estrada

• Dr. Leopoldo Lazatin

• Dr. Juanito Billote

• Prof. Julita Yabes

• Dr. Lourdes E. Abadingo

• Dr. Natividad Gervacio

• Dr. Emilie Flores

• Dr. Josefina G. Tayag

• Dr. Marie Josephine De Luna

• Dr. Nymia Pimentel-Simbulan (2014-2023)