Founded in 1965 as CD Calahorra Promesas, the club acted as a reserve team of CD Calahorra and played intermittently in the regional leagues until the club decided to close the reserve section in 1995.[2][3][4] They returned to an active status in 1998, playing four seasons in the Regional Preferente before again folding.[5]
In 2004, Calahorra reached an agreement with AF Calahorra to become their farm team, and in June 2011, the latter was fully integrated in the former's structure, being renamed to CD Calahorra B.[6][7] In the following year, however, the club opted to use the Juvenil squad as their reserve team, and the B-team became inactive.
Calahorra B returned to action in 2018, and immediately achieved promotion to Tercera División in May of the following year.[8]