Chouinard compiled a 104-60-13 record with the Shawinigan Cataractes and was selected by the Ottawa Senators in the first round (15th overall) of the 1998 NHL Entry Draft. By 2000, unable to agree to terms on a contract with the Senators, he instead opted back into the NHL draft. Hoping for a fresh start with a new organization, Chouinard was instead selected once more by the Senators, this time in Round 2 (45th overall) of the 2000 NHL Entry Draft.
