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Founded in 1999 as ŽNK Odranci, the club won its first Slovenian Cup title in 2005 and the Slovenian League championship the following year, competing under the name ŽNK Pomurje. The next season, Pomurje won its second cup and was the league's runner-up. In 2008 and 2009, Pomurje was second to ŽNK Krka both in the league and the cup, but declined in the next two seasons (third in 2010 and fifth in 2011).

However, in 2012, Pomurje won both the league title and the cup, attaining their first double. The club became a dominating force between 2012 and 2016, winning four doubles and five straight championships. In the 2018–19 season, Pomurje won a seventh championship title without dropping any points, winning all 21 games of the season.

In the 2014–15 UEFA Women's Champions League season, Pomurje advanced to the round of 32 for the first time by finishing as the best runner-up in the qualifying tournament.

In December 2022, ŽNK Pomurje announced its merger with the men's football club NŠ Mura. The process was completed in January 2023, when the club adopted the new name ŽNK Mura, and also changed its colours to black and white.