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Founded in 1997 by Iain Johnston and Paul Johnston, for the initial two seasons of its existence the club was under the auspices of Preston Athletic. The name changed to Hibernian Ladies in 1999 and they became one of the leading women's teams in Scotland. After being temporarily voted out of the Scottish Women's Premier League by its other member clubs in 2005 after officials failed to attend the body's AGM (subsequently downgraded to a warning and small fine), in 2006–07 Hibs secured a domestic double, finishing the league campaign with a 100% record. The club has won the league championship three times and then represented Scotland in the UEFA Women's Cup. In that competition they failed to progress beyond the first round in each instance, finishing second twice and third once in the group stage.

Hibernian won the Women's Scottish Cup in 2010, for the fifth time in eight years. The team's success in the national cup competition was in contrast to their male affiliate, who had not won the Scottish Cup for over a century until their victory in 2016.

In January 2011, six Hibernian players were called into the Scotland women's national football team. In May 2011 Hibernian beat local rivals Spartans 5–2 in the Scottish Women's Premier League Cup final.

Hibs won domestic cup doubles in 2016, 2017 and 2018.

Ahead of the 2020 season, the club was rebranded as Hibernian Women and offered their first part-time professional contracts. The senior team was fully integrated into the men's club in July 2022, with the youth sides still being run by the Hibernian Community Foundation.