The club was founded in 1934, but disbanded during World War II. After being reformed in 1956 they joined the Maidenhead & District League. The club later transferred to the Hayes & Giles League. They were Premier Division champions in 1998–99 and again the following season. After winning the league for a third time in 2001–02, they moved up to Division One East of the Hellenic League. In 2010–11 the club were Division One East Champions, earning promotion to the Premier Division. The season also saw them win the league's Floodlight Cup and Challenge Cup.
Despite not finishing in the relegation zone, Holyport were voluntarily demoted to Division One East at the end of the 2014–15 season after their manager left and they were unable to find a replacement.