APMCFI was founded in 1967 with the seven (7) existing medical schools and the UP Institute of Public Health as founding members.  With the goal of ensuring quality medical education, its initial activities were voluntary accreditation of the schools and the formulation of core courses in the different disciplines.  It formulated policies and standards for medical education which were adopted by the Board of Medical Education (BME).

At present, the Association is represented in the Technical Committee for Medical Education (TCME) of the Commission on Higher Education. It is a participant in the external accreditation of the MD Program of medical schools under the Philippine Accrediting Association for Schools, Colleges & Universities (PAASCU) as well as the Health Human Resource Network which was created by the Department of Health.