During the early years of the Second World War, the heads of a number of medical schools would meet to discuss solutions to wartime problems relating to medical education. In 1947, this group was formally established as the Conference of Deans of Provincial Medical Schools. This enabled greater communication between medical schools on issues surrounding the role of doctors and how they could be trained to meet the health needs of the United Kingdom, particularly in relation to the National Health Service, which was founded in 1948.

The Conference of Deans of Provincial Medical Schools consisted of medical schools from Cambridge, Bristol, Liverpool, Durham, Birmingham, Cardiff, Manchester, Leeds and Oxford. All members of the group agreed that the conference should serve a purely advisory function and remain autonomous from the medical schools it represented. At the same time, a separate conference was formed by medical schools in the London area. This was called the Conference of Deans of London Medical Schools.

Though separate, the two conferences would frequently hold joint meetings. Over the decades the issues faced inside and outside of London became more similar, and increasingly they required a single, national voice to address them. In 1989, the two conferences merged to become the Conference of Deans of UK Medical Schools.

In 1991, this became the Council of Heads of Medical Schools. It was during this time that the council became affiliated with the Committee of Vice Chancellors and Principals, now Universities UK, and for the first time employed professional policy staff in order to increase the capabilities of the organisation. At this point it moved from being a forum for discussion to a body which could undertake its own work on behalf of all medical schools.

Finally, in 2006, the organisation changed to its current title of the Medical Schools Council. Since that time the council has seen significant expansion in its areas of operation. The MSC Assessment Alliance was formed in 2011 as a means of developing a common resource for medical schools to draw from in planning their assessments, and which demonstrates common standards between medical schools to the regulator. In 2015 the MSC Selection Alliance was formed to carry out national work in admissions and widening participation.

With its various groups made up of national experts in different areas of medical education, the council now works as an expert advisory body, improving policy and shaping the future of medicine in the UK.