Founded in 1929, Castilleja played in regional leagues until 2015, when the club achieved a first-ever promotion to Tercera División.[3] The club spent three consecutive seasons in the division before suffering relegation in May 2018.[4]
In May 2020, Castilleja returned to the fourth division,[5] but suffered immediate relegation. In May 2025, the club returned to a national division after achieving promotion to Tercera Federación.[6]