Sir Harry Burns, a former NHS Greater Glasgow Director of Public Health, has campaigned extensively on inequalities and called for greater emphasis on spending on early years to give children a better start in life.
He is leaving the top medical job after eight years for a professor role at Strathclyde University, where he will work closely with academics in Lyon, France, also specialising in inequality.
Sir Harry will become Professor Of Global Public Health and will begin his new job in April. He said he was looking to devote more time to research into inequality in health.
He added: "I have enjoyed the challenges over the past eight years and have had the opportunity to do a lot of work around health inequalities.
"I am looking forward to being able to develop my interest in health inequalities further, and continuing to contribute towards building a better public health landscape."
Last year Sir Harry said the decline of industry in Glasgow, including the shipyards, led to the growing health inequalities. He said the jobs in the yards and engineering works were never replaced and the void was filled with drink, drugs and violence.
He said smoking and poor diet were not to blame for higher death rates in Glasgow.
Scottish Health Secretary Alex Neil praised Sir Harry's contribution and his handling of some serious issues during his time as Chief Medical Officer.
Mr Neil said: "I would like to thank Sir Harry for the significant contribution he has made to health across Scotland.
"Over the past eight years, he has provided leadership in a range of areas, from leading the response to the H1N1 swine flu pandemic in 2009, to providing health advice about Legionnaires disease.
"In particular, Sir Harry has brought a renewed focus to the issue of health inequalities within Scotland, and I am delighted his new role will enable him to continue his focus in this area.
"It has been a pleasure working with Sir Harry and I wish him every luck for the future."
Sir Harry Burns was a general surgeon in Glasgow through the late 1970s and the 1980s when he became a consultant surgeon at the Royal Infirmary.
After a spell in health management he became Director of Public Health with Greater Glasgow NHS in 1993 and was given the post of chief Medical Officer in 2005.
In 2011 he was knighted.