Following its foundation, the club quickly won the national championship, and has subsequently dominated women's football in the country, winning 12 consecutive titles. The club has participated in the UEFA Women's Cup from 2003 onwards but never reached the final rounds. In the 2009–10 UEFA Women's Champions League, when the competition was rebranded and reorganized, the side started in the round of 32 but lost to Russia's Zvezda 2005 Perm 8–0 on aggregate. In the next two years the team had to go through the qualifying phase, failing both times, but in the 2012–13 UEFA Women's Champions League they managed to qualify after hosting the qualifying phase in Sarajevo and defeating two clubs which played the round of 32 of the previous season of the Women's champions league.
On 4 July 2015 the club signed an agreement on long-term cooperation with Bosnian men's football club FK Sarajevo, by which SFK 2000 assumed the latter's maroon and white colors, club logo and kit.  FK Sarajevo board members will enter the SFK 2000 board, by which the two clubs will de facto function as one.