Zulte Sportief was founded in 1950 and directly became a member of the national association (matricule n° 5381). The club Zultse V.V. (with the same matricule) was started after the 1976 merger between Zulte Sportief and S.K. Zulte. In 2001, the team merged with K.S.V. Waregem, who had played in the first division for many years. No team from Zulte ever achieved promotion to the second division before S.V. Zulte Waregem in 2002. Zultse V.V., though, gained access to the third division in 1995. The club finished 14th out of 16 for two seasons and was relegated the second time after the playoff.

In 1999, the season in which it came back, Zultse finished 4th in this division. Two years later, the new club became champion of the 3rd division A. The registered office of Zulte Waregem lies in Zulte but the club is based in the stadium of K.S.V. Waregem in Waregem and the red and white colours of K.S.V. Waregem prevail.

The club got a chance to shine on the European stage during the 2006/07 season, reaching the Round of 32 of the UEFA Cup, facing off against English club Newcastle United, although they lost 4-1 on aggregate.