In their first season in Division Three North of the new Peterborough and District Football League, their first match was a 5–2 defeat away to Paston Athletic Reserves.

In the 2000/01 season, Eye United won all thirty league games, winning the title by sixteen points.

They joined the United Counties League Division One in 2003/04, moving from Lindisfarne Road to their current base in Dogsthorpe.

In the UCL Premier Division, the club finished its debut season in ninth place and a couple of years later reached the quarter finals of the FA Vase, before losing to the eventual victors, Dunston, 4–3 in front of over 600 spectators, and following the departure of manager Chris Plummer that team broke up, and the seasons since 2012 have seen frequent changes of manager and playing staff.

Despite this, success continued to be achieved at all levels from juniors to youths and reserves in 2014/15, the Star first team secured its second Hinchingbrooke Cup with a victory over Deeping Rangers and reached the final again the following year, where we were defeated by Peterborough Sports.