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The club was founded as Voetbalclub Sint-Eloois-Winkel Sport in 1940, during the Second World War. Initially, they played in the Catholic Flemish Sports Association, a league that competed with the Royal Belgian Football Association (KBVB). In 1946, they joined the KBVB as Sint-Eloois-Winkel Sport and started out in the Belgian Provincial Leagues. The club moved through the provincial leagues and from 1964 to 1983 they played in Eerste Provinciale – the highest provincial tier – for 19 consecutive years. After that, however, the club declined somewhat, until they even had to fight for retention in the Third Provincial division. In the mid-90s, however, the club would rise through the ranks again. At its 50th anniversary in 1991, the club became "royal", adding koninklijke to their name.

In 1995, Winkel Sport won the title of the Third Provincial and was promoted to Second Provincial again. Two years later, in 1997, they could also return to Eerste Provinciale. Another two years later, in 1999, they also took second place in Eerste Provinciale, again behind Wervik. However, due to the merger of KSK Roeselare and KFC Roeselare to K.S.V. Roeselare in the national division, an extra spot became available, and Sint-Eloois-Winkel Sport were able to promote through this. For the first time the club reached one of the national tiers.

Sint-Eloois-Winkel made its debut in Belgian Fourth Division with a fifth place. The second season was more difficult, but in its third season in Fourth Division, the club finished third and was allowed to go to the play-offs for the first time. Verbroedering Meerhout proved too strong there. The club also held its own in the following seasons and usually ended in upper half of the league table. In 2007, Winkel Sport finished second and therefore qualified for play-offs again. After a win against K. Lyra, they were eliminated this time by La Louvière. In 2008, they ended up at the top again. Winkel Sport had finished with the same number of points as SC Wielsbeke, but with a worse goal difference. Wielsbeke thus became champion, Sint-Eloois-Winkel missed out on the title, but again qualified for play-offs. After a win over Sporting Hasselt, however, they were also eliminated there again, this time by RFC Union La Calamine. In 2008–09, Winkel Sport competed for the title for the third year in a row, but for the third time in a row they ended in second place. And as with the previous years, this time too, it was not possible to force promotion through the play-offs. This time, the team was eliminated by Sporting Hasselt.

In 2014, the club won in the final play-off round against OMS Ingelmunster and KVK Westhoek, but lost to KSC Grimbergen. However, due to the bankruptcy of RWDM Brussels, an extra place in Belgian Third Division became available, so that Sint-Eloois-Winkel Sport reached promotion nonetheless.

In April 2019, Sint-Eloois-Winkel Sport won promotion to the Belgian First Amateur Division after finishing first in their division.