In 1952, the Board of Trustees, under the chairmanship of Don Jose Cojuangco, commissioned a Medical School Committee to recruit faculty members and establish the institute.

[2] The Institute's courses were handled by luminaries in Philippine medical education, with Dr. Liborio Gomez in Pathology, Bacteriology, Parasitology and Laboratory Diagnosis; Dr. Daniel de la Paz in Pharmacology; Dr. Perfecto Gutierrez in Medicine; Dr. Gloria T. Aragon in Obstetrics and Gynecology; Dr. Carlos Sevilla in Ophthalmology and Otorhinolaryngology; Dr. Fe Del Mundo in Pediatrics; Dr. Tomas M. Gan in Hygiene, Preventive Medicine and Biostatistics; and Dr. Ricardo L. Alfonso in Surgery.

Together with the School of Medical Technology and the FEU Hospital, IM was re-constructed and made into a non-stock, non-profit educational foundation.

With the installation of its Board of Trustees, chaired by Nicanor M. Reyes Jr., FEU-NRMF gained full independence of its operations and management from the main university.

In 1995, due to the lack of space and the need of expansion of the institution, the Board of Trustees approved the relocation of FEU-NRMF to a 1.5-hectare (3.7-acre) lot in Fairview, Quezon City, with a new campus and hospital planned to be constructed.

Operated by the foundation, the FEU-NRMF Institute of Medicine continues its tradition and excellence, serving as a premier medical school in the country.

[9][10] The Institute of Medicine Building is located at the left end of the complex's main facade, housing all learning spaces for its students.

[11] On December 22, 1996, FEU-NRMF Chairman Josephine S. Cojuangco-Reyes presided over the groundbreaking of the new P500 million medical school and hospital complex, assisted by Dr. Ricardo Alfonso, and Dr. Philip S. Chua.

[3] In 2023, Healthway Medical Network (HMN), the hospital and clinics division of Ayala Healthcare Holdings Inc. (AC Health), established a partnership with the institution.