Lewes remained in Division One of the Isthmian League until being relegated to Division Two at the end of the 1990–91 season. Although they were promoted back to Division One the following season after finishing as runners-up in Division Two, they were relegated again in 1992–93 and again in 1993–94, dropping into Division Three. The club were Division Three runners-up in 2000–01 and were promoted to Division Two. The following season saw the club reach the first round of the FA Cup for the first time; drawn at home to Stoke City, the match was moved to the Britannia Stadium with Stoke winning 2–0. The club finished the season by winning the Division Two title to secure promotion to Division One South;