Atlas was founded in a bar in Guadalajara, Mexico, where a few friends recalled their friends experience while studying at
Ampleforth College in
North Yorkshire, England. In August 1916, Alfonso and Juan José "Lico" Cortina, Pedro "Perico" and Carlos Fernández del Valle, the three Orendain brothers and Federico Collignon (who had studied in Berlin) finally decided to set up a football team. They chose the name "Atlas" based on the
Titan of
Greek mythology of the
same name, and chose red and black as the club's colours to mimic those of
Ampleforth College whose patron saint, St Lawrence, was also chosen as the patron saint of Atlas. The red signifies the blood of St Lawrence and the black signifies his martyrdom. Occasionally the crest of Ampleforth College is seen hanging from a banner in the stadium. The first title for the club was the
Copa MX in
1945–46, where they beat
Atlante in the final. That same year, they won the supercup (league vs. cup champion) against
Veracruz 3–2. Four years later, Atlas won their second Copa MX, in the
1949–50 season. The following year, in the
1950–51 Mexican Primera División season, Atlas won its first league title, with twelve wins in 22 matches. However, just two years later, Atlas was relegated for the first time after losing 4–0 against Tampico. But the following season, Atlas made an immediate return to the top flight. Atlas had a golden age in the late 1990s under the management of
Ricardo La Volpe, with promising players such as
Rafael Márquez,
Daniel Osorno,
Juan Pablo Rodriguez,
Pavel Pardo,
Mario Méndez,
Omar Briceño, and
Miguel Zepeda, but even though they had a team with enormous talent and reached the
Verano 1999 final, they couldn't conquer the title and lost against
Deportivo Toluca in a match defined by penalties after a 5–5 draw on aggregate and with extra time. In
2000, Atlas participated in the Copa Libertadores for the first time. They began their campaign in a round-robin preliminary stage where they played against Club America,
Deportivo Táchira, and
Deportivo Italchacao. Their first match was a 2–0 loss to America, followed by draws against Tachira and Italchacao. However they would recover and finish top of the group after beating America 6–3 and then beating Tachira, followed by a draw against Italchacao. As a result, Atlas gained entry into the proper competition in group 4 alongside
River Plate,
U. de Chile and
Atletico Nacional. The Guadalajara-based club's first match was on 23 February, a 1–1 draw against River. Their next match was a 3–2 win against Atletico Nacional in
Medellín. The club then drew against U. de Chile and lost to River, followed by a 5–1 rout of Colombian champions Nacional, but a loss in their final match against U. de Chile in
Santiago. Although Atlas finished level with U. de Chile on points, a better goal difference would see them go through. In the round of 16, the Mexican club defeated Colombian club
Atlético Junior 5–1 on aggregate and were through to the quarter-finals, where their run would end after losing twice to eventual runner-up
Palmeiras and being eliminated 5–2 on aggregate. In
2008, Atlas made their second appearance in the Copa Libertadores. Their campaign started with a qualifying tournament called InterLiga where they faced Toluca, Morelia, and America. At the end of the InterLiga they were tied on points and goal difference with Toluca, so a coin toss decided who would advance to the next round. Atlas won the coin toss and advanced to the first stage, where they defeated Bolivian club La Paz 2–1 on aggregate. In the group stage with
Boca Juniors,
Colo-Colo, and
Maracaibo, Atlas finished first with eleven points, including notable victories against Boca Juniors and Colo-Colo. In the round of 16 they would eliminate
Lanus 3–2 on aggregate. In the quarter-finals, they were matched up with Boca Juniors again. In the first leg, played in
Buenos Aires, Atlas secured a 2–2 draw, but in the second leg in Guadalajara, Boca won 3–0 and eliminated the club. Atlas qualified for the
2015 Copa Libertadores after finishing second on the table in the 2014 Apertura. The team was led by
Tomás Boy and was matched up in the group stage with
Independiente Santa Fe,
Atletico Mineiro, and
Colo-Colo. In their first match they lost 1–0 to Santa Fe, but in the second match they had a historic 1–0 victory against Atletico Mineiro in Brazil, which ended a 37-year undefeated home streak for the club in the Copa Libertadores. Atlas later beat Atletico again at home, but exited the competition with a last-placed finish in the group and a loss to Santa Fe in
Bogotá. On 12 December 2021, Atlas ended a 70-year title drought when they defeated
Club León at the Estadio Jalisco via penalties 4–3 and won their second league title. On 5 March 2022, during a match between Atlas and Querétaro at Querétaro's stadium,
a riot broke out between fans attending the match. Videos posted on social media showed groups of men beating, kicking, dragging and stripping victims. According to the
Querétaro state civil protection agency, at least 22 men were injured. The Liga MX sanctioned Querétaro by banning Querétaro-affiliated
barras from attending home matches for up to six months in response to the riots. Atlas were awarded a 0–3 win for the game which was abandoned at 0–1. Atlas won its third league championship on 29 May 2022 against Pachuca. In the first leg on 26 May, Atlas defeated Pachuca at Estadio Jalisco 2–0, and although they lost the second leg 2–1, they won 3–2 on aggregate to become only the third team in league history to win back to back titles. In July 2025, Grupo Orlegi announced that it had put Atlas up for sale due to Liga MX regulations that sought to end multi-ownership of teams after the 2026 FIFA World Cup. In April 2026, the purchase of the club by Grupo PRODI, a company headed by José Miguel Bejos, who also owns
Pericos de Puebla, a baseball team, was announced, with the company taking possession of the team starting on 1 July 2026. ==Youth Academy==