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The club was established in 1893. In 1909–10 they won the Advertiser Cup and the Swindon Junior Cup. Three years later the Advertiser Cup was won for a second time. The club later joined the Cirencester & District League and were Division Two champions in 1931–32. They then moved to the Swindon & District League, winning both the Division Three title and the Swindon Junior Cup in 1933–34. The club won the Division Three title again in 1954–55, the first of four successive titles that saw them win Division Two the following season, Division One in 1956–57 and then the Premier Division in 1957–58.

Highworth retained the Premier Division title the following season, also winning the Advertiser Cup and the Faringdon Thursday Cup. They went on to dominate the league in the 1960s, winning the Premier Division title in 1960–61, 1961–62, 1962–63, 1963–64, 1965–66, 1966–67 and 1967–68. They also won the Wiltshire Senior Cup for the first time in 1963–64. The club then joined the Wiltshire Combination, finishing as Division Two runners-up in 1970–71, earning promotion to the Premier Division. In 1976 the Combination merged with the Wiltshire League to form the Wiltshire County League, with Highworth becoming members of Senior Division One.

In 1978–79 Highworth finished bottom of Division One and were relegated to Division Two. Although they were promoted the following season, they were relegated again at the end of the 1980–81 season. A third-place finish in Division Two in 1982–83 saw the club promoted to Division One, and after finishing tenth the following season, they were accepted into Division One of the Hellenic League. They won the Division One Cup in 1988–89.

Highworth remained in Division One until a third-place finish in 1993–94 resulted in promotion to the Premier Division. They won the Supplementary Cup in 1998–99 and were Premier Division runners-up the following season before winning the league in 2004–05. The club won the Challenge Cup in 2011–12. The 2014–15 season saw the club reach the semi-finals of the FA Vase, eventually losing 3–0 on aggregate to North Shields. After finishing third in the Premier Division in 2017–18, they were promoted to Division One South of the Southern League. They were transferred to Division One Central for the 2022–23 season, but finished third-from-bottom of the division and were relegated to the Premier Division of the Hellenic League.