Although Canvey Island were relegated back to Division Two at the end of the 1996–97 season, they were Division Two champions in 1997–98 and Division One champions in 1998–99 as successive promotions saw them reach the league's Premier Division. In 2000–01 they finished as league runners-up, and also reached the second round of the FA Cup; the first round saw them beat Second Division Port Vale 2–1 in a replay at Vale Park after a 4–4 draw at Park Lane. In the second round the club were drawn at home to near-neighbours Third Division Southend United; in a game switched to Southend's Roots Hall, they lost 2–1. However, the club's biggest success came in the FA Trophy, where they reached the final at Villa Park after beating three teams from the Football Conference. In the final the club beat favourites Forest Green Rovers 1–0, becoming the first team from the Isthmian League to win the competition for 20 years. The following season saw them finish as Premier Division runners-up again, as well as reaching the third round of the 2001–02. After winning 1–0 against Football League clubs Wigan Athletic and Northampton Town in both the first and second round, they lost 4–1 at Burnley in the third round.