East Preston FC was originally formed in 1947, but folded within 10 years. It was reformed, as the present club, in 1966 when it was elected to the Worthing League.

The club then moved on to the West Sussex League for the start of the 1968–69 season before becoming founder members of the newly formed Sussex County League Division 3 in 1983, having won a number of honours in the seasons leading up to that. Division 3 was won at the first attempt but the club were unable to take their place in senior football as the ground and facilities were not up to the required standard. The club remained in Division 3 until 1990–91 when they gained promotion once again, this time as runners up to Ifield. However this lasted just one season before being relegated back the following year. After a couple of near misses they finally achieved promotion again at the end of the 1994–95 season. In that promotion season they achieved a memorable treble also winning the Division 3 Cup and the Sussex Intermediate Cup.

In 1997–98 promotion to Division 1 was gained for the first time in the club’s history. The club acquitted itself well for two seasons, finishing fourth in 1999–2000 before a season of crisis saw them relegated in 2000–01. Recovery however, was swift + East Preston were immediately promoted back to the top flight. Season 2003–04 saw the club once again a force in Division 1 challenging and leading the division for parts of the season before finally finishing a creditable 3rd, losing out on the runner-up spot only on goal difference. A couple of years consolidation followed before a 4th place finish under Chris White lead to some renewed optimism, however with White's departure to Horsham YMCA East Preston were relegated the following season and continued to under achieve in Division 2.

Prior to the 2011/12 season East Preston appointed manager Dom Di Paola from Worthing United bringing with him his assistants Ian Brown, Jan Miller, Mick Wannacott and Adam Westwood.