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The club was established in 1924. They became members of the Surrey Intermediate League, winning the league title in 1935–36. However, by the 1970s the club were playing in the Woking & District League. They won the league's Charity Cup in 1972–73 and went on to win the Premier Division, League Cup and Charity Cup treble in 1978–79. The club were Premier Division runners-up the following season, but retained the League Cup and Charity Cup, as well as winning the Challenge Cup.

Knaphill then returned to the Surrey County Intermediate League (Western), joining Division Three. They were Division Three champions their first season back in the league, earning promotion to Premier Division Two. In 1981–82 the club were runners-up in Premier Division Two, securing a third successive promotion. The following season saw them finish as runners-up in Premier Division One. In the 1990s the club absorbed Heathlands from the Guildford and Woking Alliance League.

In 2005–06 Knaphill won Division One of the Surrey County Intermediate League (Western) and were promoted to the Premier Division. The following season they were Premier Division champions, earning promotion to Division One of the Combined Counties League. A third-place finish in Division One in 2013–14 saw the club promoted to the Premier Division. In 2017–18 they won the Premier Challenge Cup, beating Worcester Park 3–2 in the final.

In 2023-24 season, Knaphill finished third in the Combined Counties League Premier Division South. They beat Tadley Cavella 2-0 in the play-off semi-final on 4 May, only to lose 2-1 at home to AFC Croydon Athletic in the final on 7 May 2024.

On 8 May 2024, joint managers John Cook and Jamie Daltrey resigned, along with assistant Lee Trussler.