Horndean were established in 1887 and played their first match against Red Star (from Havant not Belgrade) on October 27. The club only played friendlies until the First World War when they joined the Waterlooville & District League.

The Deans were able to earn plenty of success winning the league four times before joining the Portsmouth League. They won the second division in 1954 to earn promotion to the Premier Division, where between 1968 and 1971 they won three league titles.

In 1972, Horndean entered the Hampshire League and played in the fourth division. Two back-to-back promotions saw the club enter the Hampshire Division Two for the first time and then promotion was finally earned to the first division in 1980.

Horndean became a founder member of the Wessex League in 1986, however struggled to make any progression in the league with the club finishing in the bottom half nine seasons in a row. In the 1994-95 season, Horndean suffered relegation to the Hampshire League and were outside the Wessex League for the first time since its inception.

However, the Deans would finally return to the Wessex League in 2004 as founder members of the newly devised Wessex Division Two. In 2010-11 the club finally returned to the Wessex Premier Division as they finished runners up in Division One.

Horndean has continued to rise up the Wessex League and in 2016-17 the club appointed Michael Birmingham as manager. The club under Birmingham has managed to finish sixth, fourth and second, their highest ever finish in the Wessex Premier Division.