Born in Lévis, Quebec, Claude, the son of Thérèse (née Pouliot) and Raoul Auger, was educated at Laval University, where he graduated magna cum laude with a bachelor's degree in Health Sciences.
Auger completed post-graduate training from 1978 to 1983, also at Laval University, in General Surgery, and became a Fellow of the Royal College of Physicians and Surgeons of Canada.
His first posting was to Canadian Forces Base (CFB) Halifax as a General Duty Medical Officer and then subsequently to Lahr, Germany in 1975.
In 1978, he was promoted to Major shortly before returning to Laval University to complete post-graduate training in General Surgery.
In the summer of the same year, Auger was transferred to Ottawa, as Chief of Surgery at the National Defence Medical Centre (NDMC), a position he held until 1996.