Founded in 1923 and re-established in 1997, the club has played in the Meistriliiga since 2008 and have never been relegated from the Estonian top division. Nõmme Kalju has won 1 Meistriliiga and 1 Estonian Cup trophy.
Nõmme Sports Club Kalju was founded on 20 December 1922. Nõmme Kalju Football Club was founded in 1923 by two professional wrestlers, Aleksander Šneider and Mart Liiv. Their home ground was Hiiu Stadium in Nõmme and club was active until World War II.
Nõmme Kalju football club was re-established in 1997 by former Estonia national football team manager Uno Piir, Õhtulehe Noorte Jalgpalliklubi president Anton Siht and Värner Lootsmann. The squad was formed from Tallinna Jalgpallikool and Õhtulehe Noorte Jalgpalliklubi youth players and competed in the III Liiga.
Nõmme Kalju played in the III Liiga for eight seasons in a row. In 2002 the current President Kuno Tehva acquired the club with a goal of establishing a professional football club. The club won promotion to the third division II Liiga in 2004 and in 2005 to the second division Esiliiga. In 2006, the club was unsuccessful in the battle for promotion to the Meistriliiga, eventually finishing behind Kuressaare and Tallinna Kalev. During the the 2007 season, Nõmme Kalju hired a Brazilian manager Getúlio Fredo. On 18 November 2007 Nõmme Kalju lost the first promotion and relegation game to Kuressaare 0–1 but won the second one away 2–1 on 24 November 2007 and won the promotion to the Meistriliiga thanks to the away goals rule.
In 2008, the aim was set at achieving the national championship within 5 years, alongside promoting youth football. Preparing for the next season in the Meistriliiga, Nõmme Kalju brought in 16 new players with four of them being former internationals. The season began well, with Nõmme Kalju competing for the top positions. The club finished the season in fifth place but after TVMK Tallinn disbanded, the club was awarded fourth place with just one point away from the third place. In the 2009–10 season the team participated in the UEFA Europa League first qualifying round for the first time in their history but were eliminated by Latvian Dinaburg.