He played in the Quebec Major Junior Hockey League from 1984 to 1988, each year with a different team. In 1984-85 he was with the Shawinigan Cataractes; in 1985-86 Hull Olympiques; in 1986-87 Longueuil Chevaliers; and in 1987-88 Victoriaville Tigres. Despite his team changes, Desjardins won several league awards, including leading goalie in 1985-86 and 1986-87, most valuable player in 1986-87, and defensive rookie in 1984-85.