FC Wageningen finished 18th in the clubs first Eredivisie season and as such were relegated back to the Eerste Divisie immediately.

In 1980 the club would get promoted to the Eredivisie again but once again finished last place the following season and as a result were relegated back to the Eerste Divisie again.

Its first success came on 18 June 1939, when the team won the KNVB Cup by defeating PSV Eindhoven (2–1 after extra-time) in Arnhem.

Nine years later, on 19 June 1948, FC Wageningen once again won the Cup, this time by a win over DWV.

FC Wageningen played its last match in professional football in May 1992 against NAC Breda.