Zaragoza CFF was founded in 2002 after carrier company Transportes Alcaine bought Inter Aragón, which played in the lower categories. In 2005 the new team promoted to Superliga Femenina, the Spanish top league. After Grupo Prainsa became the main sponsor in 2007 and renamed the club as Prainsa Zaragoza, the main team consolidated itself in the first half of the table.
In 2009 the club performed their best season to date, ending 5th and playing the 2009 Copa de la Reina final. In the Cup competition, Alcaine lost to Espanyol.
Transportes Alcaine repeated success in 2013 by reaching their second Cup final. As in the previous final, the club was defeated by a four-goal margin, this time 0–4 against FC Barcelona.
On 26 September 2016 the club changed its name to Zaragoza Club de Fútbol Femenino.