The club has spent majority of its history in the second and third tiers of French football, with short spells in the top flight.

The club faced bankruptcy in 2011 and subsequently reformed in the sixth tier; since then it has aimed to climb back up the league pyramid.

Upon the club's creation, it earned the nickname Les Forgerons (The Blacksmiths), due to having strong support from the commune's local steelworks area.

In 1974, inspired by playmaker Casimir Nowotarski, Gueugnon reached the second division promotion play-offs, but lost to Rouen.

In 2000, Gueugnon shocked French football supporters around the country after winning the Coupe de la Ligue.

The following season, Gueugnon played the UEFA Cup but lost to Greek club Iraklis 1–0 on aggregate in the first round.

The resulting outcry led to the town, club, and support of Gueugnon developing a hatred towards their nearby foes.

Not only because the two clubs are relatively close to each other or because they have been in the same division for a long period of time, but also because Gueugnon sent Louhans down by holding them 1–1 on the last day of the Ligue 2 season in 1984–85.