The club was formed in 1960, playing firstly in the Manchester and Wythenshawe League. They moved to the Lancashire and Cheshire League in 1963, winning the Third Division at the first attempt. They moved to the Manchester League in 1973, finishing as runners-up in 1978–79, 1981–82 and 1985–86. 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. 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. In 2003–04 they finished in fifth place in Division Two. The following season though they finished in 18th after having 21 points deducted. They were promoted back to Division One in 2005–06, finishing as runners-up. In 2006–07 they finished in 13th place and also reached the fourth round of the FA Vase. In 2007–08 they finished in 8th place. The club dissolved in 2013 after poor supporter attendance. Since 2012–2013, AFC Flixton, a Manchester-based Sunday League team now play their homes games at Valley Road. They are representatives of the Manchester Accountants Football League winning the First Division title in their first season.
As of 9 March 2009, the average league-game attendance at Valley Road for the 2008–09 season was 41, which placed Flixton 21st for the division, and was a decrease of 31.8% from the previous season. Past averages:
