The club was founded on 22 October 1930, and has played exclusively at amateur level in all its history.

Genemuiden was part of the Hoofdklasse league in the 2009–10 season, which it completed in fifth place in the Saturday C group, then winning promotion to the newly established Topklasse league for the inaugural 2010–11 season through playoffs.

After being relegated in 2012–13 to the Hoofdklasse, it returned to the Topklasse by winning the Saturday C title the next season.

In the 2021–22 season, Genemuiden qualified for the promotion playoffs, but lost 3–2 on aggregate to SC Feyenoord in the first round.

However, in the promotion final, Genemuiden lost 6–1 on aggregate to Excelsior Maassluis, and remained in the Derde Divisie.