The ANU Medical School can be viewed as a descendant of the University of Sydney’s Canberra Clinical School. Prior to its inception in 1993, students from University of Sydney, University of NSW and University of Queensland had been coming to Canberra to complete placements at Woden Valley Hospital for several years. Under the guidance of Professor Paul Gatenby, the Canberra Clinical School developed a strong teaching program to the point of conducting the entire final year of University of Sydney’s five year undergraduate medical degree.

When the University of Sydney introduced a four year graduate program in 1996, the school became responsible for training 20 students in the entire years three and four curriculum and parts of years one and two. During this time, the school also took the first steps toward its current reputation for cutting-edge medical research, establishing laboratories, a tissue and organ museum and an animal house at the Canberra Hospital.

By 2000, the School had become so successful the then Minister for Health, Michael Wooldridge, deemed that ANU should establish a stand-alone medical school. The current ANU Medical School was formed in 2002 with the appointment of Professor Gatenby as Foundation Dean and funding from the Commonwealth Department of Health & Ageing.

Building on the University of Sydney's curriculum, the school increased the importance of rural and Indigenous health, ethics and law, the social aspects of medicine and medical science. The first 72 students of the then Bachelor of Medicine / Bachelor of Surgery (MBBS) graduated in 2007.

The School has helped drive the development of first class health services in the ACT, improving medical care for the community. The School continues to attract eminent medical researchers and educators to the region as well as medical practitioners from right across all specialties who see the presence of a medical school in the city as being important in their decision to practice here. The current Dean, Professor Imogen Mitchell,  continues to strengthen the School’s first-class curriculum and internationally recognised medical research program.

In 2009 the Commonwealth Government further increased the intake to 90 domestic students. In January 2014 the Australian Medical Council approved ANU Medical School changing its medical program from the Australian Qualifications Framework (AQF) Level 7 program resulting in the award of the MBBS degree, to the AQF Level 9 Extended program resulting in the award of the MChD or Medicinae ac Chirurgiae Doctoranda (Latin for Doctor of Medicine and Surgery) degree.