The college started functioning in December 1962 as the third government-run medical college in Kerala. The college which initially functioned in the District Hospital, Kottayam from 1962 to 1970 was shifted to Arpookara in April 1970.

In 1975, all clinical departments were shifted to the newly constructed campus at Arpookara, now named Gandhinagar. The same year, the nearby ESI Hospital was taken over to start the children’s hospital: Institute of Child Health. A new administrative B block was started in 1985. In 1996, the C block was added which houses the departments of Pharmacology, Pathology, Microbiology and the Central Library.