The club was the result of the merger between Stade Mouscron and A.R.A. Mouscron in 1964.
R.E. Mouscron had financial problems during the 2004–05 season and so the president and mayor of Mouscron Jean-Pierre Detremmerie left the club and was replaced by Edward Van Daele. The players with the higher wages were asked to leave the club, as did Marcin Żewłakow, Franky Vandendriessche, Geoffrey Claeys, Koen De Vleeschauwer and Alexandre Teklak.
On 28 December 2009, Mouscron announced its third forfeit in a row because of enduring financial problems, and was thus, according to Belgian league rules, excluded from competition, with all its previous results in the ongoing competition being scrapped. The club in its current form ceased to exist, with all its players (and staff) becoming free agents.