Founded in 1923 and re-established in 1997, the club has played in the Meistriliiga since the 2008 season and have never been relegated from the Estonian top division. Nõmme Kalju has won 1 Meistriliiga and 1 Estonian Cup trophy.
Nõmme Kalju football club was founded in 1923 as a division of the Nõmme Sports Club Kalju (Estonian: Nõmme Spordiklubi Kalju) by two professional wrestlers, Aleksander Šneider and Mart Liiv. Their home ground was Hiiu Stadium in Nõmme and the club remained active until the World War II.
In 2002, Kuno Tehva acquired the club with a goal of establishing a professional football club. Nõmme Kalju were promoted to the third tier II liiga in 2004 and in 2005, to the second tier Esiliiga. Nõmme Kalju finished their first season in the Esiliiga in 5th place. In 2007, Brazilian Getúlio Fredo was hired as manager. Nõmme Kalju finished the 2007 Esiliiga season in 6th place and faced Kuressaare in promotion play-offs. The club lost their first match home 0–1 but won the second leg away 2–1 and advanced to the Meistriliiga on away goals.
By winning the Meistriliiga, Nõmme Kalju also qualified to the 2013–14 UEFA Champions Leaguequalifying phase. Nõmme Kalju beat HJK in the second qualifying round 2–1 on aggregate, but was subsequently defeated by Viktoria Plzeň 2–10 on aggregate in the third qualifying round. The team failed to defend their Meistriliiga title in 2013, finishing as runners-up, despite Vladimir Voskoboinikov winning the goalscoring title with 23 goals. Nõmme Kalju finished the 2014 Meistriliiga season with a disappointing 4th place, following which the manager Igor Prins was sacked and replaced by former Nõmme Kalju and national team player Sergei Terehhov. Under Terehhov, the team had a successful start, winning first 9 league games and winning their first Estonian Cup trophy, defeating Paide Linnameeskond 2–0 in the 2014–15 Estonian Cup finals. On 12 September 2015, Terehhov resigned after poor results in the Meistriliiga, with Getúlio Fredo taking over as caretaker manager. Nõmme Kalju finished the 2015 Meistriliiga in third place. On 4 November 2015, it was confirmed that Sergei Frantsev would be hired as manager after the season. Nõmme Kalju reached the third qualifying round in the 2016–17 UEFA Europa League, but failed to improve results in the Meistriliiga, finishing the 2016 season in third place again.