FC Juárez was founded on May 29, 2015, by a group of businesspeople led by
Alejandra de la Vega. She previously managed
Club de Fútbol Cobras, a now-defunct football team from Ciudad Juárez that was owned by her father, Federico de la Vega. That same year, FC Juárez returned to Liga MX, Mexico's top-tier professional league, for the first time since 2012, following the relegation and eventual disbandment of the previous franchise,
Indios de Ciudad Juárez. On June 7, 2015, it was officially announced by the
Ascenso MX officials that FC Juárez would compete in the Ascenso MX, starting in the
Apertura 2015 season. On December 5, 2015, after a very successful beginning to the season, the team ended the 2015 campaign in second place, and FC Juárez captured its first Ascenso MX title after beating
Atlante 3–1 on aggregate, thus gaining the right to play in the promotional final in the Ascenso MX. The failed to qualify for the
Clausura 2016 liguilla and lost the promotional final against
Necaxa. The following season, Juárez failed to qualify for the liguilla. In the
Clausura 2017 season, Juárez lost the final against
Lobos BUAP with an aggregate score of 4–2. For the
2017–18 Ascenso MX season, the league announced that Juárez was one of six
Ascenso MX teams eligible for promotion to the
Primera División de México the following season. In the
Apertura 2017 season, Juárez lost their second consecutive final, against
Alebrijes de Oaxaca, on penalties. On June 11, 2019, Juárez replaced
Lobos BUAP in the
Primera División after the founding bi-national group purchased the struggling franchise and relocated it to Ciudad Juárez, thus returning top-level football to Ciudad Juárez. They have developed a friendly, cross-border rivalry with
El Paso Locomotive of the
USL Championship since that side began play in 2019. FC Juárez achieved its best Liga MX performance in the
Apertura 2025, finishing eighth in the league table and qualifying for the play-offs (
liguilla) for its first time in history. The club was eliminated in
the quarter-finals by
Toluca, the defending champions, losing 1–2 on aggregate. FC Juárez lost the first leg at home 1–2 and drew 0–0 in the away match. Toluca went on to win the tournament. ==Stadium==