Prior to the foundation of the Scottish Council on Postgraduate Medical Education in 1970, governance of postgraduate medical education in Scotland was carried out by regional committees drawn from the Royal Colleges, University medical schools and the National Health Service. Following the Royal Commission on Medical Education report (often called the Todd Report) in 1968, the Scottish Council on Postgraduate Medical Education (SCPME) was established in 1970 with the purpose of co-ordinating, funding and advising on postgraduate education and training in hospitals, general practice and clinical psychology in Scotland.

In October 1992 the SCPME was reconstituted as the Scottish Council for Postgraduate and Medical and Dental Education (SCPMDE), and in 1993 it became a Special Health Board of the NHS. NHS Education for Scotland was established as a Special Health Board by Statutory Instrument 2002 No. 103, The NHS Education for Scotland Order 2002. The staff and functions of SCPMDE, including the South East of Scotland Postgraduate Medical Deanery, transferred to the new body in April 2002, together with those of the National Board for Nursing, Midwifery and Health Visiting and the Post Qualification Education Board for NHS Pharmacists in Scotland.