After almost sixty years as a Lancashire Combination club, they were made founder members of the Northern Premier League in 1968.
After winning the Northern Premier League Cup in 1971, the club languished in the lower half of the table, finishing bottom for two successive seasons and folded in 1976 because of financial difficulties.
They reached the final of the FA Vase in 1985, losing 3–1 to Halesowen Town in front of a 16,000 crowd at Wembley.
Re-formed in 1997 as Fleetwood Wanderers, the club was placed back in Division One of the North West Counties Football League (now the tenth tier of the English League system) and a sponsorship deal saw the club's name immediately changed to Fleetwood Freeport F.C..
The club was promoted to the Premier Division of the North West Counties League in 1999 and renamed Fleetwood Town F.C.
In the play-off semi-finals, against AFC Wimbledon, a new attendance record of 4,112 was set in the home leg, but Fleetwood lost both games with an 8–1 aggregate scoreline.