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The league was created in 2001, with the inception of the new Superliga Femenina, composed by only group instead of the four of the previous seasons.

Since 2011, teams were divided in seven groups by geographical criteria.

• Group 1: Asturias, Cantabria and Galicia.
• Group 2: Basque Country, La Rioja and Navarre.
• Group 3: Aragon, Balearic Islands and Catalonia.
• Group 4: Andalusia, Ceuta, Extremadura and Melilla.
• Group 5: Castile and León, Castile-La Mancha and Community of Madrid.
• Group 6: Canary Islands.
• Group 7: Region of Murcia and Valencian Community.

The league was renamed as the Primera Nacional de Fútbol in 2019 after the RFEF renamed the new division between it and the first tier as Segunda División Pro, after initially naming it Primera División B.

In early 2022, it was confirmed that the league structure would be altered again, after only three seasons: the existing Primera División would be a standalone professional league of 16 teams, a single nationwide 16-team division known as the Primera Federación would be created as the second tier, the existing Segunda División Pro of 32 teams (two regionalised 16-team groups) would become the third tier and be named the Segunda Federación, and the existing Primera Nacional division of 96 teams (six regionalised 16-team groups) would become the fourth tier. These levels would be administered by the RFEF and more closely resemble the men's post-2021 structure, albeit only one professional league and six fourth-tier groups rather than five. The fourth level was renamed the Tercera Federación FUTFEM prior to the 2023–24 season.