The club was founded in 1991 by a group of gay footballers including amateur player Aslie Pitter MBE, after Mikko Kuronen put an advert in a gay publication asking for like-minded people to contact him if they were interested in a kickabout on a Sunday.

[4] The club's stated mission is "to be a driving force in helping tackle discrimination in the game" be it "homophobia, transphobia or biphobia".

[10] In more recent times the club was promoted back to the Middlesex County Premier Division for the 2017–18 season, but were relegated.

[12] The club also played in the Football for Everyone Cup at The Emirates in 2014, and against Manchester United's LGBTQ+ fan group, the Rainbow Devils, at Old Trafford in 2019.

In November 2023, Stonewall won the Gay Games for a record 5th time, defeating Seattle 3–2 in the final.

The Men's 1sts play in blue, the 2nds in red, and the Unity and Women & Non Binary side in a top made up of the colours of the Trans flag.