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The club was established in 1907 and joined the High Wycombe and District League. They went on to win the league twelve times, as well as winning the High Wycombe Senior Challenge Cup twelve times. In 1950 the club moved up to Division Two of the Great Western Combination, which they won at the first attempt to earn promotion to Division One. This was renamed the Premier Division in 1954, and the club were runners-up in 1956–57 before winning the league in 1957–58. They were champions again in 1962–63. However, the league folded at the end of the 1963–64 season, resulting in the club returning to the High Wycombe and District League.

In 1974–75 Flackwell Heath won both the Reading Senior Cup and the Berks & Bucks Intermediate Cup. In 1976 they moved up to Division One of the Hellenic League and were runners-up in their first season in the division, earning promotion to the Premier Division. In 1982 they switched to the Athenian League, but it folded at the end of the 1983–84 season, with the club joining Division Two North of the Isthmian League instead. At the end of the 1984–85 season they were transferred to Division Two South, where they remained until league restructuring saw them placed in Division Three in 1991. The division was renamed Division Two in 2002, and when it was abolished in 2006, the club were initially due to be transferred to the Spartan South Midlands League, but East Ham United folding led to the club being restored to the Isthmian League and placed in Division One North.

The 2006–07 season saw Flackwell Heath finish bottom of Division One North, resulting in relegation to the Premier Division of the Hellenic League. They won the league in 2014–15 and were set to be promoted to Division One Central of the Southern League. However, after Clevedon Town were demoted, they were provisionally placed in Division One South & West and subsequently declined promotion due to increased travelling costs. In 2015–16 the club won the Berks & Bucks Senior Trophy, beating Newport Pagnell Town 2–0 in the final. At the end of the 2020–21 season they were transferred to the Premier Division of the Spartan South Midlands League. After a single season in the Spartan South Midlands League, they were transferred to the Premier Division North of the Combined Counties League.