The club was founded in 1942 as merger of two local clubs, Union Sportive de Carquefou and Jeanne d'Arc de Carquefou, the latter being a sports team whose football section was founded three years earlier.

During the 2007–2008 season, Carquefou had a very successful Coupe de France campaign, reaching the quarter-finals in the competition after having defeated Olympique Marseille in the round of 16 despite the club's amateur status.

Carquefou finally won Group D of CFA and promoted to Championnat National once in 2011–12 season.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.