Nõmme Kalju FC traces its roots back to 1923, although the modern club dates from its re-establishment in 1997. The original team was founded as a division of the Kalju Sports Club by two professional wrestlers, Aleksander Šneider and Mart Liiv, and had already played in Estonia's top division between 1925 and 1927. The club's activities were halted by the Soviet occupation of Estonia in 1944, when its clubhouse was destroyed by the first Soviet tank to enter the Nõmme district.
The team represents Nõmme, a green and distinctive district of Tallinn that has maintained a strong local identity over the years, and that connection with the neighbourhood remains one of the most important parts of Kalju's character. The club plays its home matches at the compact Hiiu Stadium, holding only a few hundred spectators, giving matches a very different atmosphere from the larger venues used by Tallinn's biggest clubs. Also symbolic is the so-called Railway Derby against long-standing rival FC Flora — named after the fact that the train stations nearest to each club's ground, Kitseküla and Hiiu, sit barely half a kilometre apart.
The club's greatest sporting achievements followed its re-establishment by former Estonia national team manager Uno Piir, together with Anton Siht and Värner Lootsmann. After promotion to the top flight in 2008 and the club's acquisition by its current president, Kuno Tehva, Nõmme Kalju won the Estonian championship for the first time in 2012, repeating the feat in 2018. The club's honours also include two Estonian Cup triumphs (2014–15 and 2024–25) and two Estonian Supercups (2019 and 2026). Known to fans as Roosad Pantrid (Pink Panthers) for its distinctive black-and-pink colours, the club has established itself as an important alternative to Estonia's traditional Flora–Levadia rivalry, and made its mark in Europe by eliminating Finnish champions HJK Helsinki en route to the 2013–14 UEFA Champions League qualifying phase.