Keith Pearson, who was appointed chairman of the NHS Confederation in May 2010, was also knighted for his services to the NHS.
Meanwhile, district nurse Dorothy Davies has also been awarded an OBE for her services to healthcare in Llandrindod Wells, Powys, while Susan Morgan, a Macmillan clinical nurse specialist, was awarded an OBE for her services to healthcare in Wales.
Eleanor Robertson, Greenock, Renfrewshire, was awarded an OBE for her services to community healthcare.
The GMC's chief executive Niall Dickson said of Professor Rubin's award: 'This is richly deserved and is recognition of a highly distinguished career in medicine and research, as well as a great contribution to medical education and regulation.
‘It also reflects well on the GMC and what Peter has achieved in the years he has served this organisation.'