Lewes Football Club was formed at a meeting at a local pub (The Royal Oak) in 1885 and initially wore green shirts designed to evoke the surrounding South Downs. The present red and black kit was adopted in 1893.

They won the championship of the Mid Sussex League twice before World War I. After the first World War the club played in the Brighton, Hove & District Football League, until the end of the 1919/20 season when they became one of the founder members of Sussex County Football League. They were runners-up on four occasions but it was not until 1964/65 that they were finally able to win the championship, after which they stepped up to the Athenian League. The two sides met on six occasions in the Athenian League Division One between 1965/66 and 1967/68 with Lewes having the better of the encounters, winning three (including an 8-1 victory) and drawing two. After winning the Division 2 title in 1968, promotion to the Premier Division followed just two years later when the club won the Division One title. For 1973/74 the Premier Division was dropped and we met again in Division One (Bay had been promoted as champions of Division Two in 1970/71), both games were drawn, and Herne Bay finished bottom of the table and moved to the Kent League. There was also a FA Cup First Qualifying Round clash in 1990/91, Lewes winning 1-0 at Winch’s Field.

In 1977 Lewes joined the newly expanded Isthmian League, initially in Division 2. Promotion to Division 1 came in 1980 but in 1991 the Rooks were relegated. They bounced back at the first attempt but could only manage one season at this level before two successive relegations saw them in Division 3, where they actually finished second from bottom of the entire league on two occasions. From 1998/99 the club claimed two consecutive promotions, taking them to the Isthmian League Division One South. in the 2003/04 season they were champions of this division and stepped up to the unprecedented heights of the Conference South after a busy schedule of playoffs at the end of the season, in effect jumping two divisions.

They reached the play-offs in both the 2004/05 and 2005/06 seasons, finishing 4th in the league on both occasions. In the 2007/08 season they won promotion to the Conference National for the first time. On 25 March 2009, Lewes' relegation from the Conference National was confirmed after 39 games of the season, with the club finishing bottom of the league. The 2009/10 season was again a struggle for Lewes, numerous winding-up orders were battled off the field, safety was finally secured with a 2–1 away win against Hampton and Richmond on the final afternoon of the season. On July 9, 2010 The Rooks became a member-owned club with six founder members of the new Rooks 125 group forming the inaugural Board of the new Lewes Community Football Club ownership body

Following a poor start to the 2010/11 season, despite some impressive results, their relegation to the Isthmian League was confirmed on the 25th April 2011. The Rooks were demoted from the Isthmian League Premier Division to Division One South on 2 April 2016, with three games to play. Last season they ended in 9th place, beating Herne Bay twice within five days, 1-4 at home and 1-3 at the Dripping Pan. On the opening day of this campaign Bay were unlucky to lose 0-1 to a time added on goal in the 93rd minute.

The Rooks currently sit on top of the table with nine wins, three draws and just one defeat from their 13 games. Bay have a game in hand and are 10 places and 12 points below.