Flixton finished in 13th in their first season in the Northern Premier League, 1996–97 when they also reached the third qualifying round of the FA Cup. They again reached the third qualifying round of the FA Cup 1998–99. However, in 1999–2000 they finished in 21st place and were relegated back to the North West Counties Football League Division One. They struggled the following season, finishing in 20th place, just avoiding a second successive relegation. After another season of struggle in 2001–02 they were relegated back to Division Two in 2002–03 when the club's main sponsor, the managers and the first team players all left.