The current club was officially established in 1997 but, in two previous incarnations, the club’s history dates all the way back to 1908. The original club, Fleetwood F.C., were champions of the Lancashire Combination in 1923–24, and registered a hat-trick of Lancashire Combination Cup wins in 1932, 1933 and 1934. Their goalkeeper in the first of those victories was Frank Swift, who went onto become one of England’s finest goalkeepers and died in the Munich air disaster in 1958.
After almost sixty years as a Lancashire Combination club, they were made founder members of the Northern Premier League in 1968. The club finished in 10th place in their first season. As the NPL was one of several leagues immediately below the fourth division of the Football League this was effectively the fifth tier of English football, and the club would not surpass this success until 2010–11 season. Despite winning the Northern Premier League Cup in 1971, the club languished in the lower half of the table, finishing bottom for two successive seasons in 1974-75 and 1975-76 and folded in 1976 because of financial difficulties.
The club was re-established in 1977 as Fleetwood Town F.C., with many of the original personnel. Initially placed in Division One of the Cheshire League, they were moved in 1982 to the North West Counties League Division Two in its inaugural year, and promoted to Division One in 1984. 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. The club was placed in Division One (second tier) of the Northern Premier League when the league established a second tier in 1987, becoming the inaugural Division One Champions in 1988. In 1990–91 the club finished 4th in the NPL Premier Division, then effectively the sixth tier. However, by 1996, this second club had also folded.
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 2002. Tony Greenwood was appointed manager in 2003, and soon afterward, Andy Pilley took over as chairman. Successive promotions as North West Counties League champions in 2005 and Northern Premier League First Division runners-up in 2006 saw the club reach the Northern Premier League Premier Division.
In the 2007-08 season Fleetwood went on to win the Northern Premier League, gaining promotion to the Conference North. Along the way they set a new attendance record for the division, and were easily the best-supported club in the Premier Division.
Fleetwood started the 2008-09 Conference North season poorly and, with the club at the bottom of the league manager Tony Greenwood along his coaching staff was sacked. Greenwood was replaced by Micky Mellon, who also remained as Under-15 and Under-16 coach at Burnley. In January 2009 his position at Fleetwood was made full-time, a first for the club.
The demise of Farsley Celtic partway through the 2009-10 season was detrimental to Fleetwood’s campaign, as Farsley’s entire 2009–10 playing record was expunged. Fleetwood were chasing promotion along with near neighbours Southport, and the ruling cost Fleetwood three points relative to Southport. Fleetwood appealed against the decision but the appeal was rejected the day before the last match of the season, leaving Southport one point ahead. Both teams won on the final day, giving Southport the championship. Fleetwood instead had to contest the play-offs, and after beating Droylsden on penalties in the semi-final Fleetwood won promotion to the Football Conference by beating Alfreton Town 2–1 in the final.
For the 2010-11 season the club made all of its players full-time professionals, though this resulted in a few players leaving the club, including club captain Jamie Milligan. The club spent most of the season in or near the play-off positions, eventually qualifying by finishing in fifth place. 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.
The following season was very successful. In the FA Cup they reached the Third Round for the first time. After beating Mansfield Town, Wycombe Wanderers and Yeovil Town, they were drawn at home to local rivals Blackpool, but lost 5–1 to the then Championship club, with Jamie Vardy scoring Fleetwood’s only goal. In the league Fleetwood went on a 29-game unbeaten run, and were declared champions with two games remaining, giving them promotion to the Football League for the first time. At the end of the season Vardy moved to Leicester City for a fee of £1m, which subsequently rose to £1.7m, a record transfer fee for a non-league club.
Fleetwood had a good start to the 2012-13 season and had risen to third in the league after 10 games. However Fleetwood only won two of their next 10 games slipping to 6th and there was a fall out between chairman Andy Pilley and manager Micky Mellon after Mellon allegedly applied for the Burnley and Blackpool managerial vacancies. On 1 December 2012 following a 3–2 defeat against Aldershot in the FA Cup Mellon was sacked as manager of the League Two side. On 6 December 2012 Graham Alexander was appointed manager.
The 2013-14 season was another successful one. Having been in and around the automatic promotion places all season the club narrowly missed out on automatic promotion finishing in 4th place. After beating York City in the play-off semi-final, Fleetwood beat Burton Albion 1–0 in the play-off at Wembley to win promotion to League One for the first time.
Playing at the club’s highest level the 2014-15 season was the club’s most successful yet. After three games the club was top of the league for two games and apart from a couple of games remained in the top half of the league all season eventually finishing a very credible 10th place. Also in 2014 the club purchased a 57 bedroom hotel in Blackpool for the youth team and in 2015 the club started to move into its new training ground in Thornton.
The following season was a difficult season. In July 2015 chairman Andy Pilley announced that the club’s strategic direction would move more towards a self-sustaining model utilizing the development and sell-on of home-grown talent rather than to buy in players to attempt to climb the league pyramid further. The playing budget was trimmed heavily. After a poor start to the season Graham Alexander was sacked with the club one point above the relegation zone after being beaten 5–1 by Gillingham. Steven Pressley was appointed manager and after a season flirting with the relegation zone he successfully guided the club to safety
On 20 April 2016 Sir Alex Ferguson officially opened the club’s £8m Poolfoot farm training ground complex with 18 pitches including a floodlit 4G pitch, gym, cafe, bar, offices, etc.
In July 2016, Pressley resigned and was replaced by Uwe Rosler..