The club was founded in 1868, and has disbanded several times (late 1890s, 1911 and 1914) in its history. In 1975 the club merged with Wingate F. C. to become Leyton-Wingate F.C., until 1992 when the two clubs parted company and the name reverted back to Leyton. In 1995 the club merged with Walthamstow Pennant and moved away from Leyton Stadium to become Leyton Pennant F.C., now known as Waltham Forest

A new Leyton Football Club was set up in 1997, and following a High Court case in 2002, successfully won the right to be recognised as an official continuation of the original club. A statement by lawyers Richard West Freeman Christofi reads:

"Please note that by Order of the High Court Chancery Division dated 26 July 2002, in an action brought against Leyton Pennant Football Club and the Football Association, Leyton Football Club (now incorporated as a Limited Company) of Wingate Stadium Lea Bridge Road Leyton has effectively been restored as Leyton Football Club, the unincorporated club formed in 1868; has had its membership to the FA restored; has had its history dating back to 1868 restored and the order also requires Leyton Pennant to refrain in any way from holding itself out to being Leyton Football Club."[1]
At the beginning of the new millennium Leyton won back-to-back promotions, winning the Essex Senior League in 2001/02 then finishing second in the Isthmian League Second Division the following season. In 2003/04 Leyton finished second in the Isthmian League First Division North, gaining a place in the new Isthmian League Premier Division for the following season as the non-league pyramid was reconstructed. 2004/05 saw Leyton finish fifth in the Isthmian Premier Division and reach the final of the play-offs for promotion to the Conference South, but the Lilywhites were beaten 2-1 in the final by Eastleigh.

Costas Sophocleous the club chairman, was once the manager. Having managed the team for the 2003/04 and 2004/05 seasons, Sophocleous decided to step back from management to concentrate on his role as chairman. Following a bad start to the season, however, two managers were sacked in quick succession and the chairman took over the managerial role again.

Leyton F.C then appointed Troy Townsend as manager for the English 2005/06 season. He continued to manage the first team squad, the reserves side (which compete in the capital league) and the Eastern Junior Alliance U18's squad.

The 2006/07 campaign saw Leyton complete the season in 15th position. This led Troy Townsend to step aside as manager of the first team to concentrate on the reserves and U18's sides. The following season, under manager Rowley Cray, the club suffered an 11-1 home defeat to Hendon and a 9-0 loss at AFC Hornchurch en route to relegation.

Steve Newing and Del Deanus (previously at Edgware Town) were appointed as joint managers for the 2008/09 season, but resigned in November. Tony Ievoli then took the reins but he resigned at the start of September 2009, before being replaced by former Grays Athletic manager, Craig Edwards. In November 2009 Edwards was replaced by Ivan Persaud.

Ivan Persaud left the club and was replaced as manager by former player Malcolm Dannie for the beginning of February 2010.The teams inability to win a game in his tenure led to Dannie leaving and being replaced by former Ashford Town Middlesex Reserve Team manager Wilson Frimpong for the final six games of the season during which time, the team went unbeaten but still narrorly couldn't avoid finishing 21st and in the relegation zone. The club did however get a reprieve and remain in the Isthmian League Division One North division for the 2010/11 season.

After managing only one win, several of the more experienced players at the club were sold and eventually Wilson Frimpong parted with the club. Leyton unveiled Gordon Boateng as the manager to finish Leyton's season with the hope of avoiding relegation.