Audaz was founded in 1948, playing their home games at Estadio La Coyotera, a modest seating-capacity venue in the small town of Apastepeque.

On 11 February 2001, Audaz' truck carrying the entire team and staff was shot at by gang members, killing coach José Napoleón Gómez.

In its third year in the Segunda División, Audaz won the second half Clausura 2017 title, defeating Independiente FC 4–1 in a two-legged final series, which included a 3–0 victory away from home.

[4] Audaz immediately faced Independiente FC again, the champions of the first half of the 2016–17 season (Apertura 2016), in a one-game promotion playoff, winning 1–0 on a goal by Santos Guzmán.

In July 2019, after the 2018–19 season was over, it was revealed that Campos had not meet his contractual requirements of the purchase from the previous owner's group, having failed to pay the salaries of the players and staff for most of the season; the team was bankrupt, no owner existed, and the sole remaining board member officially sold Audaz' license in La Primera to Independiente FC.