Dr. David Butler-Jones says his recovery has not gone as quickly as he would have liked, and it would not be right for him to continue in the role of Chief Public Health Officer.
"I made great progress, but this job requires stamina, especially in a crisis," Butler-Jones said in an interview.
"While I've recovered a lot, and my smarts are there, I can't do that, and it's not fair to the country."
Butler-Jones said he would step down once his replacement is chosen, but will continue working part-time as advisor to the federal government.
He was dubbed Canada’s top doctor in his role as head of the Public Health Agency of Canada, and led government efforts to deal with the H1N1 scare.
The H1N1 flu struck Canada in 2009. The new strain of influenza A virus, otherwise known as swine flu, affected roughly 10 per cent of the population, resulting in the deaths of more than 400 people.
Butler-Jones suffered a stroke in May 2012. In an interview with The Canadian Press in December, he said one of his worst fears was that he would not be able to return to work.
Health Minister Leona Aglukkaq said his decision to step down for health reasons shows Butler-Jones continues to put the best interests of Canadians first.
"By doing so, he is once again showing his commitment to public health," Aglukkaq said in a statement.
Butler-Jones was the first person to be appointed to the post when it was created in 2004.
The Canadian Medical Association commended Butler-Jones for his work, saying the Public Health Agency of Canada has become an internationally recognized centre for population and public health under his direction.
"As the face of public health in Canada, Dr. Butler-Jones has spoken first and foremost for the needs of Canadians," said a CMA statement.
"His leadership and thoughtful council at the helm will be missed."
Butler-Jones has had a long career in public health, both in Ontario and Saskatchewan, where he served as the province’s chief medical health officer from 1995 to 2002.