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Although an earlier Sittingbourne United club had been playing since as early as 1881, Sittingbourne F.C. traces its lineage to 1886 when the club was reorganised under the new name. The club moved to a field behind the Bull pub in 1892, where they were to remain for nearly 100 years. Senior status was acquired in 1893, and the following year the club joined the first incarnation of the Kent League, before withdrawing to enter the South Eastern League in 1905.

After World War I the club rejoined the Kent League, where they played until 1927 when they joined the Southern League. In 1930 they left this league and it is unclear where they played next. After World War II the Brickies rejoined the Kent League once again, where they were champions in 1957–58 and 1958–59. After the second title win they rejoined the Southern League, but after a promising start their performances declined and in 1966–67, after finishing bottom, they dropped out to join the Kent Premier League which had changed its name from the Thames & Medway Combination. This lasted for one season and the league folded. In 1968 a new Kent league was formed which the club joined.

During season 1961–62 Accrington Stanley left the football league. This created a vacancy and 25 clubs applied to join, of which Sittingbourne were one. They did not obtain any votes and Oxford United were elected with 39 votes.

Sittingbourne were Kent League champions in 1975–76, 1983–84 and 1990–91, the third title win earning them a place back in the Southern League. In 1992–93, by now playing at the new Central Park ground, they won promotion to the Southern League Premier Division, however a financial crisis led to relegation two years later. Although the team bounced back, winning the Southern Division title at the first attempt, they were relegated again in 1998 as the club hovered on the brink of being wound up completely. A move out of Central Park and a drastic reduction in the playing budget saw the Brickies through their troubles, but they flirted with relegation back to the Kent League for a number of years, only finishing in the top half of the table on one occasion in the next eight seasons.

In 2006 a re-organisation of the English football league system saw Sittingbourne moved into the Isthmian League, starting in Division One South. The 2009–10 season ended with Sittingbourne winning the Kent Senior Cup for the first time in 52 years.

Gary Abbott left his position as manager in May 2011 and was replaced by his assistant Richard Brady. He brought in ex-brickie Jamie Coyle as his assistant. In September 2011 after a brief spell in charge they were offered management positions at Leatherhead and indicated that the positions were too good to turn down. Long serving player, Joe Dowley took over the caretaker position of manager with the assistance of players Bradley Spice (assistant manager) and Bryan Glover (coach). In November 2011 the committee were impressed with what had been achieved that they made their positions permanent.

Joe Dowley resigned as manager after the last game of the 2011–12 season stating that he wished to return to his playing career. in May 2012 the club employed the Scottish brothers Jim & Danny Ward as joint managers. They were previously with Ramsgate who they left in April 2012. The Ward brothers left their position in September 2013 by mutual consent .

In September 2013 after a brief successful spell as caretaker managers, Matt Wyatt and current player and captain Nick Davis were appointed joint managers. In July 2014 Nick Davis resigned as joint manager and Matt Wyatt continued as manager on his own for a short period and then resigned himself in October 2014. His replacement was his previous joint manager Nick Davis. Season 2017-18 started with only two players remaining from the previous season. A new squad was recruited and the season started on a positive note and at one point saw them reach the top of the table. However this did not last and a succession of poor results saw the team drop down the table.

In January 2018 Nick Davis resigned and was replaced by one of the coaches, Aslan Ödev, as an interim manager for the rest of the season. After much success, in April 2018 Aslan Ödev was awarded the role of manager and will continue for the 2018–19 season. The 2018–19 season started well for the Brickies but then started to go downhill with a string of poor results. In January 2019 Aslan Odev left his position and was replaced by Chris Lynch the Dover Athletic head of youth development. Results were disappointing after a good start and Chris resigned. Darren Blackburn took over in 2020.