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The club was established in 1887 and played their first match on 27 October against Red Star from Havant. They initially played at Blendworth Hill before moving to their current ground.

The club only played friendly matches until World War I, after which they joined the Waterlooville & District League, They won the league title in 1926–27, 1929–30, 1930–31 and 1931–32. They went on to join the Portsmouth League, winning Division Two in 1953–54. They were later promoted to the Premier Division, which they won in 1968–69, 1969–70 and 1970–71.

In 1972 they moved up to Division Four of the Hampshire League. By the mid-1980s they had reached Division One, and became founder members of the Wessex League in 1986. The Deans struggled to make an impact on the league and in nine seasons never once managed to finish in the top half. After finishing bottom of the league in 1994–95, they were relegated back to the Hampshire League, where they remained until rejoining the Wessex League as founder members of the new Division Two in 2004.

In 2010–11 they were promoted to the Premier Division after finishing as runners-up in Division One. In October 2015 long serving manager David Carter left the club and on Wednesday 21 October 2015 Portsmouth Academy Coach Craig Pearce and Simon Chamberlain were appointed as successors. Craig Pearce and Simon Chamberlain took the team to fifth place, Horndean's highest ever position in the Sydenham's Wessex premier league. At the start of the 2016–2017 season Horndean FC saw the arrival of Michael Birmingham, Dutchy Holland, Jason Manna, and Matthew Driver. The season finished with Horndean FC in 6th place in the Sydenham's Wessex Premier division. The 2017-2018 Season saw the first team finish in 4th place, in 2018-2019 the team under Michael Birmingham finished second, its highest ever position in the Sydenham's Wessex premier League. The club were promoted to the Isthmian League for the first time as Champions in the 2022–23 season.