[3] The club was re-established in 1997 by the former Estonia national team manager Uno Piir, Anton Siht and Värner Lootsmann.

Nõmme Kalju joined the Estonian football league system and began competing in the Northern division of the III liiga.

In 2009, the club also made its debut in Europe by playing in the 2009–10 UEFA Europa League, where they were defeated by Dinaburg 1–2 on aggregate in the first qualifying round.

The club strengthened their first-team squad significantly during the 2010–11 winter transfer window by signing Estonian internationals Alo Bärengrub, Tarmo Neemelo, Eino Puri and Kristen Viikmäe.

Nõmme Kalju finished the 2011 season as runners-up, seven points behind champions Flora, while Tarmo Neemelo scored 22 goals.

Nõmme Kalju finished the 2014 season with a disappointing fourth place, following which Igor Prins was sacked and replaced by former player Sergei Terehhov.

Less than two months later, on 25 April 2019, Frantsev was sacked after a poor start to the 2019 league season, with Roman Kozhukhovskyi taking over as caretaker manager, before being hired permanently on 14 June.

Kalju returned to Hiiu Stadium in May 2024 and finished the 2024 season in second place, with Alex Matthias Tamm winning the league's top scorer award with 28 goals.

Located approximately 8 km southwest of the Tallinn city centre and in the district of Nõmme, it has an artificial turf surface and has undergone several renovation periods, most recently in 2023–2024.

[12][13] Nõmme Kalju's deepest rivalry is with FC Flora and the fixture is known as raudteederbi (English: The Railway Derby).

The rivalry emerged in the early 2010s, when Kalju started challenging Flora in terms of on-field success, as well as in fan popularity.

Throughout the years, the rivalry has also intensified due to an enmity between Kalju's president Kuno Tehva and Flora's founder Aivar Pohlak.