He will be responsible for the National Microbiology Laboratory (NML) in Winnipeg and the Laboratory for Foodborne Zoonoses (LFZ) in Guelph, Ontario.
It follows the retirement of Dr Frank Plummer and Dr Gilmour starts from next month.
The NML is responsible for identification, control and prevention of infectious diseases.
The LFZ focuses on preventing infectious disease by looking at public health risks from interactions between animals, humans and the environment.
Dr Gilmour is currently a clinical microbiologist with Diagnostic Services of Manitoba and an assistant professor in the Department of Medical Microbiology at the University of Manitoba.
He is a past employee of the agency as director of Bacteriology and Enteric Diseases and chief of Enteric Diseases at the NML.
“I know first-hand the impactful work that the agency's laboratory teams complete with the provincial public health laboratories, with other federal departments and with international collaborators,” said Dr Gilmour.
“As I rejoin these teams, I very much look forward to our continued scientific innovation and research on infectious diseases to benefit both the health and safety of Canadians, but also the international community.”