Established in 2002 and opened in 2003 with its first dean, Dr. Glenn A. M. Catedral, it is one of the youngest colleges and academic units of the university.

The medical school produced its first topnotcher since its founding in 2003 when its graduate Jomari Rieza Biñas ranked number three in the March 2016 Physician Licensure Examination in whole Philippines.

degree modeled on a traditional medicine with Christian curriculum academic program, the only of its kind in Panay island.

[11][12][13][14] The Respiratory Therapy program under the CPU College of Medicine which was established in 2015 and had its pioneer graduates in 2019, has produced two topnotchers in the respiratory therapy licensure examination in September 2019 - Ahlia Jeshanie Eusoya Demayo (rank number 2) and Precious Ira Canlas Diamante (rank number 10).

To meet the demand of the college's growing student population, a plan is also in the pipeline of Central Philippine University administration, to build a 7 storey edifice that will house the CPU College of Medicine and the CPU Research Center for Medicine, Food Security and Agriculture.