In 1986 Flixton joined the North West Counties Football League, playing in Division Three in their first season, 1986–87 when they finished as runners-up. The following season Division Three was absorbed into Division Two and the club again finished as runners-up, winning promotion to Division One. In their first season in Division One they finished in seventh place. In 1993–94 they were relegated on goal difference. However, they bounced straight back up when they were Division Two champions the following season. They followed that up with their most successful season to date in 1995–96, winning Division One, thus achieving promotion to the Northern Premier League Division One and they reached the semi-finals of the FA Vase where they lost to Brigg Town after starting the competition in the second qualifying round.