Founded in 1992 as the women football section of an homonym football club, it became an independent club following its disappearance. In 2007 the team was promoted to the Superliga by beating SD Reocín and CD Rayco in the promotion play-offs. In its debut season L'Estartit ended in the ninth position, just one point short from qualifying for the Copa de la Reina. In 2010 it qualified for the cup, where it was defeated in the first round by Levante UD.
In 2012 L'Estartit ended fourth to last and was relegated after five years in top flight. The team was weakened and barely avoided another relegation in 2013. It returned to its previous form in 2014, narrowly missing a spot in the promotion playoffs.