In 1946 Molesey United and West Molesey Old Boys merged to form Molesey Football Club. The new club joined the Surrey Intermediate League and won the league in their first season. After moving to their new ground on Walton Road, they moved up to the Surrey Senior League in 1953. After winning the Surrey Senior Charity Cup in 1956–57, the club were league champions in 1957–58. In 1959 they transferred to the Spartan League, finishing as runners-up in the league and losing the League Cup final in 1959–60. The club won the League Cup the following season and were losing finalists in 1963–64 and 1971–72. They remained in the Spartan League until joining Division Two of the Athenian League in 1973. In 1977 the club moved leagues again, this time joining Division Two of the Isthmian League.