JK內姆梅區聯

The club was founded in 2000 by Enn Loog and was initially named FC Elion, before the name was changed to FC Nõmme United in 2006. From early years on, Mart Poom, who at the time was playing in the Premier League, contributed to the growth of the club. After Poom's retirement, Mart Poomi Jalgpallikool (English: Mart Poom's Football School) was founded which started to act as an academy to Nõmme United. The club quickly established itself as one of the leading youth academies in the country. In 2018, goalkeeper Karl Jakob Hein joined the academy of Arsenal F.C. and made his first team debut on 9 November 2022, becoming the second Estonian to feature for the Gunners after club's president Mart Poom.

After finishing first in the Estonian third-tier Esiliiga B in 2019, the club was promoted to Esiliiga. After the 2022 season, Vladimir Vassiljev became the manager of the club and Nõmme United set their sights on gaining promotion to Premium Liiga within the next three seasons. They did it in one, as the club finished the 2023 Esiliiga season in first place with 90 points. After the end of the season, Vassiljev left for abroad and Nõmme United appointed Finnishman Jani Sarajärvi as head coach for their debut season in the Estonian top flight.