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From 2003, Osasuna's women's team played in Groups 1 and 2 of the Segunda División for seven seasons, usually finishing mid-table. Marta Unzué, who would later win several titles with FC Barcelona Femení, began her career at the club. In the early 2010s, some controversies arose over the organization's management of the team: in March 2011, eleven players left the team accusing the executives of sexism, lack of interest and poor training conditions, and in May of the following year, outgoing chairman Patxi Izco declared women's football as "unsightly" and "unsuitable for women".

The team was disbanded in June 2014 in the midst of financial turmoil, weeks after the male team's relegation to the Segunda División; rising star player Maite Oroz moved to Athletic Bilbao Femenino on a free transfer. However, within weeks an agreement was secured with fledgling club Mulier FCN [eu], based in nearby Mutilva Baja (Aranguren), to collaborate on the formation of a senior team in the Navarre Regional League (third tier) for the following season, with this squad playing at Osasuna's Tajonar Facilities and Mulier operating its own club structure and youth teams.

The Mulier-Osasuna team won promotion at the first attempt, winning 26 of their 28 matches. Struggling at the bottom of the table in the subsequent Segunda División campaign, the two clubs thereafter parted ways, with Mulier reprieved to remain in the second tier and Osasuna's team re-launching independently in the level below as the figureheads of a new foundation involving several other local clubs (including SD Lagunak, who for much of the decade prior were one of the elite clubs of Spanish women's football).

Mulier, who declined to join the Osasuna group as it would have resulted in their relegation, performed better without the assistance of their professional neighbours, finishing runners-up in the Segunda División group (they later agreed a new partnership with Athletic Bilbao in 2019), while the separate Osasuna Femenino team dominated the Navarre regional league (80 points from a possible 84) and were promoted to join their former partners, along with the women's sections of the Basque clubs Eibar and Alavés.

The first home fixture of 2017–18 was played at El Sadar Stadium, home to the Osasuna men's team, marking the first occasion that the venue hosted a women's match in its 50-year history.

Osasuna was also permitted to add a B team in the Navarre regional league for 2017–18, as they had previously in the 2011–12 and 2012–13 seasons. At the same time as the first team were promoted to the new Segunda Pro level in 2019, the B team also moved up to the third tier, now called Primera Nacional.

From 2018 until 2020, the telecommunications firm Euskaltel was the main sponsor of the Osasuna Femenino team. Technology company Humanox became the sponsor in 2020.

In the 2020–21 season, played in a two-phase format due to the COVID-19 pandemic in Spain, Osasuna challenged for promotion to the Primera División for the first time, but finished second behind Alavés (who also had never reached the top tier previously) in both the winter and spring regional groups.

Osasuna competed in the Copa de la Reina for the first time in the 2021–22 season after the competition was opened up to clubs outside the top division; however the lost in the first round to PM Friol (Galicia) who had been relegated from the second tier at the end of the previous campaign.