Guadalajaraa was founded on 30 January 1947, playing its first match in the amateur league against Real Ávila CF, a 2–1 win. In 1970 its grounds, Pedro Escartín (in honour of a former referee), were inaugurated.
On 18 July 1985, on the day of the club hymn's official presentation, the club first appeared in the Copa del Rey, against Rayo Vallecano. It would spend the first sixty years of its existence in the fourth division and the regional leagues.
On 4 June 2013, shortly before the second division season was over, Guadalajara was dropped back to the third category after a two-year spell even though it eventually finished above the relegation zone, due to alleged financial irregularities.