[2] The university received its first teaching hospital on an 1875 order of King Alfonso of Spain, setting up instruction in the Franciscan hospital San Juan de Dios, established in 1577.

During the war, San Juan de Dios was converted to hold the Quezon Institute and St. Paul's Hospital given to the university, but the campus and hospital were destroyed in February 1945 during the Liberation of Manila.

With supplies purchased from the United States Army and money borrowed from Elizalde and Company, the university built a new facility.

The hospital was early in offering genetic counseling to patients in the Philippines, with a prenatal diagnostic clinic opening in 1984.

The management decided to retrench its non-essential staff[4] but has deferred from pushing through with the move.