This Government Medical College was started at first as an extension wing of SCB Medical College, Cuttack in the year 1961 with an annual intake of 40 students. In 1962 it started functioning at Berhampur as a medical college and in 1966 as a hospital. “Berhampur Medical College” as it was known at its inception, was subsequently, renamed as “Maharaja Krishna Chandra Gajapati Medical College” after the Late Maharaja of Parlakhemundi, Ganjam who was committed to the cause of Orissa. The construction of the medical college building was started in the year 1966, the foundation stone of which was laid by Late Dr. P.V. Jagannath Rao, the then Minister of Health, Govt. of Orissa 1963. The construction of the building was completed and formally inaugurated by Late Sri. R. N. Singh Deo, the then Chief Minister of Orissa on 21st February 1969. The college was shifted to the new building in the same year. The foundation stone of the hospital building was laid in 1963 and the hospital that was functioning in the then District Head Quarters Hospital, Berhampur shifted to the partially constructed building in 1973. Prof. Sukumar Das, an eminent surgeon, an able administrator and excellent teacher was the Principal of this college during the formative period i.e. 1963-1973. Though he was the Principal, but actually he was the main architect of this institution. 

The admission strength was increased to 75 in 1962, 100 in 1963, 107 in 1984 and to 150 in 2008. The MBBS Degree of the college under Berhampur University has been recognised by the Medical Council if India in the year 1969. Post graduate coursed in Physiology, Genaral Medicine and surgery were started during the session 1971-72. In 1972-73, PG courses in the subjects of Pharmacology, Pathology, SPM, Paediatrics, Orthopaedic Surgery, ENT, Ophthalmology, Obstetrics and Gynaecology and Anaesthesiology were started. The PG courses in Anatomy, FMT and Biochemistry were started during the session 1974-75, 1977-78 and 1979-80 respectively. MKCG Medical College, during its more than fifty years of existence, has produced a large number of doctors, specialists, super specialists  who have worked and are working  in different parts of the country and abroad. The strong academic and practical foundations built during their study in this institution have enabled them to prove their professional excellence in different specialities not only in India but also in different parts of the world. In 2016 the Government of India has given the Letter of Permission for increase of MBBS seats from 150 to 250.