The original Clacton Town was established on 27 October 1892 and joined the North Essex League in 1895. They won Division Two in 1898–99 and 1899–1900, as well as the Essex Junior Cup in 1900. They were then promoted to Division One, but folded at the end of the 1900–01 season. A group of former players formed Old Clactonians, who joined the Harwich & District League in 1902. They remained in the league until 1905, when they were renamed Clacton Town and joined the Clacton & District League, winning it in their first season. The club then returned to the Harwich & District League, and also joined the South East Anglian League in 1907, winning Division Two in 1907–08.

In 1908 they joined the East Anglian League and the Colchester & District League, winning Division Two and the Division Two cup of the latter in 1909-10,[3] and the former in 1910–11. In 1912 the club folded for a second time, but were re-established the following year. They rejoined the Essex & Suffolk Border League (as the Colchester & District League was now known), remaining in it until 1934. During this period the club also played in the Ipswich & District League from 1921 until 1924, and again in 1927–28. In 1934 they left the Border League to join the Ipswich & District League. In 1935 they were founder members of the Eastern Counties League, finishing as runners up in 1936–37. The following season they switched to the newly established Essex County League, finishing bottom in its only season before returning to the ECL in 1938. In 1948 the club turned professional and in 1952-53 finished as runners-up for a second time.[4]

In 1956-57 the club won the East Anglian Cup and reached the fourth and final qualifying round of the FA Cup, but lost 3-2 at home to Yiewsley. After finishing fifth in 1957–58 the club moved up to the South-East Division of the Southern League. Although they finished second from bottom in their first season, the following year they won the newly renamed Division One, and were promoted to the Premier Division. In their first season in the Premier Division they reached the first round of the FA Cup for the first, and to date only time, but lost 3–1 at home to Southend United. However, after finishing twenty-first out of 22 clubs in 1962–63, they were relegated back to Division One, and after a mid-table finish in 1963–64, returned to the Eastern Counties League.

The club finished as runners-up in their first season back in the league, a feat repeated in 1974–75, a season in which they again reached the final qualifying round of the FA Cup. They also won the League Cup in 1974. They remained in the Premier Division until the end of the 1991–92 season, in which they finished second from bottom, and were relegated to Division One. They returned to the Premier Division as Division One champions in 1994–95, and won the Eastern Floodlit Cup the following season. They were relegated again in 1997-98, but won the Division One Cup and Division One at the first attempt to make an immediate return. In 2000 they won the East Anglian Cup for a second time, and in 2002 won the League Cup.

In 2005–06 the club failed to win a league match all season, finishing bottom of the Premier Division with only a single point and a goal difference of -159. Despite the poor performance, they were not relegated as two clubs (AFC Sudbury and Bury Town) were promoted from the league and one club from Division One (Fulbourn Institute) were refused promotion. Although they improved the following season, finishing twenty-first with 38 points, they were relegated to Division One.

On 15 June 2007 the club was reborn as FC Clacton, a community interest company. They returned to the Premier Division as Division One runners-up in 2009–10.FC Clacton was announced on 15 June 2007 following the end of Clacton Town Football Club - after a long and distinguished 115-year history, having been formed in 1892.

Four new owners, all local men, inherited Clacton Town Football Club Ltd in 2006, which was registered with The FA as being in control of the whole football club known as Clacton Town FC. For many reasons they were uneasy with this Ltd Company holding the club registration. Also, being a normal limited company the Club did not qualify for any tax breaks, business rates relief, etc. They were never Officials, Directors or connected to this Ltd Company in any way. The previous Directors of Clacton Town FC Ltd decided to resign from the company and informed Companies House of this that eventually resulted in Companies House striking off the Ltd Company for not submitting accounts and for having no Directors or Secretary.

The time was therefore right for a complete shake up of how the club was to be administered a new start with a clean slate. A new club was formed and FC Clacton was born. This club is run by FC Clacton CIC, which is a community interest company, set up to run the senior teams and bar. All other teams, the changing rooms and ground is administered by FC Clacton CASC Ltd. As a Community Amateur Sports Club.

The club entered it's first season playing in the first division of the Ridgeons Eastern Counties League in 2007-08 with former Colchester United and Fulham player John Reeves and David Coyle as joint first-team Managers as the club embarked on a new beginning. The first-team finished in tenth place in this first season but just six points off a promotion place. But for some horrendous injuries throughout the season, promotion at the first time of asking may well have been possible. Reeves reverted back to his sole role as Physio towards the end of the season and Coyle went alone into the 2008-09 season to push on for a return to the premier division.

2008-09 saw us finish 7th in the league but with a good progress in the FA Cup, Essex Senior Cup and FA Vase that saw a record-equalling run in the competition by reaching the fourth round proper for the first time since 1974-75.

The 2009-10 pre-season saw Paul Hillier awarded a Testimonial, having been with the club since 1998-99 with the exception of a short spell with Wivenhoe Town and a match against Ipswich Town Reserves was his reward. The visitors won 7-2 in front of 452 spectators.

That same season saw us clinch promotion as runners-up back to the Ridgeons League Premier Division after an absence of three years and in the process, we recorded a record FC Clacton win on Saturday 3 April 2010 when we beat Downham Town 9-0. We also scored our highest number of league goals ever in a season - 117. To cap a great season, we reached our first-ever cup final as FCC and beat Halstead Town 2-1 in the First Division Knockout Cup at Millfield, home of Hadleigh United.

During the close season of 2010 David Coyle stepped down as manager and was replaced by Steve Pitt. There were also a number of influential player departures which led to a very different squad starting the new season. Despite the upheaval survival was assured comfortably, ending with a 16th place finish. Shortly before the 2011-12 season got underway Steve Pitt was approached by Stanway Rovers and left to become their new manager with Andy Taylor taking over the reins. Despite another almost complete turnover of the playing squad we again battled well and finished the season in 15th place.

Taylor departed early in the 2012-13 season with Ray Turner appointed to replace him. But with another unsettled season on the pitch just four league games were won which saw The Seasiders finish bottom of the table, only avoiding relegation due to the league’s restructuring.

The start of the 2013-14 season was an exciting time that saw the club reach the FA Cup 2nd qualifying round whilst being followed through their four rounds by the BT Sport TV cameras. When Turner resigned in December 2013 he was replaced by Phil Yearling but he in turn only lasted four matches before being removed from his position. Under 18s manager Glenn Eldridge was named caretaker manager and he steered the club to safety and a 15th place finish. On the back of this Eldridge was named permanent manager for 2014/15.

However, following a run of defeats, Eldridge was dismissed with David Coyle returning in October 2014 for a second spell in charge. Late in the season the club were staring relegation in the face before a run of 16 points from 7 games saw us preserve our Premier Division status. The 2015/16 season saw great progress with Coyle’s squad securing the highest finish since the formation of FC Clacton ending the season with a top-half finish in 10th position.

The summer however saw a complete change as David Coyle departed followed by almost the entire First Team squad. Tom Gooder was appointed to replace Coyle but after eight consecutive losses to open the season, Gooder also left the club with Kieron Shelley appointed as the first team manager. The Seasiders ended the year in the relegation zone but were reprieved by a league restructure that kept them in the Premier Division.

The 2017-18 season saw the club take their place in a 24 team Thurlow Nunn Premier Division. Kieron Shelley departed as manager in February following a poor run of results, with Tom Austin appointed as caretaker boss until the end of the season. The team eventually finished in 18th position, and their place in the Premier Division was confirmed for at least another year following the FA's shake-up of the non-league pyramid.

Austin was confirmed as manager for the 2018-19 season, guiding us to a top six finish, our best-ever as FC Clacton. The following season saw us reach the Third Round Proper of the FA Vase, before the league season was prematurely curtailed due to the Covid-19 pandemic.

October 2020 saw Austin move on to take the reins at Brightlingsea Regent. The club moved quickly to appoint former Chelsea player Mark Nicholls as our new First Team Manager. His first job was to appoint Kevin Coyle to the assistant’s role. Season 2020-21 was again ended prematurely due to Covid-19. An FA restructure at the end of the season saw the club moved laterally to the Essex Senior League.

The club's first season in the Essex Senior League ended in a seventh-placed finish. Nicholls and Coyle departed the club in October, and they were initially replaced by David Collis and Rob Budd, however they parted company with the club a little over a month into the role and in turn were replaced by the returning duo of Tom Austin and Ryan Salter after their spell at Brightlingsea Regent came to an end. After a strong finish to the campaign, Tom and Salts will be looking to build as we head into the 2022/23 season.

The 2022/23 season saw the Seasiders enjoy their best campaign in nearly 50 years, finishing fourth in the Essex Senior League and runners up in the Peter Butcher Memorial Trophy, narrowly losing out 1-0 to Redbridge in the final.

Hopes were high going into last season. Tom Austin stepped down as Manager in September, replaced by Ryan Salter. A new squad of players made good progress, before Salter opted to step down in February. Mick Hanna stepped up as caretaker manager to steer the ship through the remainder of a difficult campaign, with the club finishing in 17th place.

Hanna and club legend Sean Hillier form the management team leading a new group of Seasiders into the 2024/25 season.

Alongside the First Team, the club runs 29 youth teams, four girls’ teams, and a ladies team. We also run a Reserve team and an A team, both of which compete in the Essex & Suffolk Border League.