Cruz Azul was founded under the name Club Deportivo Cruz Azul as an amateur team on 22 March 1927. The founders were the workers of cement maker Cemento Cruz Azul; the team played in the town of Jasso (now part of the "city cooperative" Ciudad Cooperativa Cruz Azul) in the state of Hidalgo. Cemento Cruz Azul was the only official sponsor until 1997, and remains a primary sponsor today.
After the death of his father at the age of 12, Guillermo Álvarez Macías began working at Cemento Cruz Azul in 1931 as an automotive mechanic. Over the course of two decades, Álvarez Marcia rose through the ranks in the company, eventually being appointed the general manager on December 10, 1955. Under the leadership of Álvarez Macías, a self-proclaimed socialist, and with the help of the clubs founder, Carlos Garcés reconstructed and invested in the company's football team to provide workers with better living conditions found success in national amateur tournaments, representing the state of Hidalgo.
Following the club's success, a stadium was decided to be constructed for the club and broke ground in 1960 in the town of Jasso, Hidalgo. The construction of Estadio 10 de Diciembre was completed in 1963 and was named after Álvarez Macías's date of appointment to general manager of Cemento Cruz Azul.
Jorge Marik, a Hungarian coach who previously managed Atlas and Atlante, signed on to manage the club in 1961. Cruz Azul won a direct promotion to Primera División after Marik led the club to the 1st position on the general table with 45 points (19 wins, 7 draws, and 4 losses) in the 1963–64 Mexican Segunda División season.
The club's success in the amateur circuit allowed the company to justify investing the club to play the professionally. The club's first professional game was played April 2, 1961, in the 1960-61 Mexican Cup against Zamora, ending in a 3-3 draw. The club was offically registered to compete in the nation's second tier professional league for the 1961-62 season.
Marik left the club after the 1965–66 Mexican Primera División season where Cruz Azul finished in 13th place out of 16 teams on the league table. Walter Ormeño became the team's interm coach, managing 3 games, before the club signed assistant manager Raúl Cárdenas to Marik on October 20, 1966.
In December 1969, Cruz Azul was entered in a non-FIFA sanctioned intercontinental cup against Manchester United organized by UEFA and CONCACAF. The winners of the UEFA Champions League and CONCACAF Champions' Cup competed in a two-legged tie. The first leg, played in Estadio Azteca on the 18th of December, Cruz Azul won 3-0 with goals by Fernando Bustos, Octavio Muciño, and Rafael Hernández Pat. The second leg played in Old Trafford on December 26 ended in a 1-1 draw with goals scored by Bobby Charlton and Octavio Muciño on the English and Mexican side respectively, winning the UEFA-CONCACAF Cup for Cruz Azul.
Founded in Jasso, Hidalgo, the club moved officially to Mexico City in 1971, where it had already registered a great presence and activity since its beginnings. Estadio Azteca, the nation's largest sports venue, served as their home venue until 1996, when they moved to the Estadio Azul. After 22 years the team returned to the Azteca at the conclusion of the 2017-18 Liga MX season. Its headquarters are in La Noria, a suburb within Xochimilco in the southern part of Mexico City.
On December 18, 1976, Guillermo Álvarez Macías died of a heart attack at the age of 56 while awaiting President Portillo for a meeting.
Vucetich also lead Cruz Azul to a Copa México title, winning the 1996–97 Copa México at the Estadio 10 de Diciembre after defeating Toros Neza 2-0. Under the management of Luis Fernando Tena, Cruz Azul won the CONCACAF Champions' Cup on August 24, 1997 for the second consecutive year after defeating LA Galaxy 5-3 in the final. Cruz Azul then went on to win the Invierno 1997 league tournament in December. After an aggregate score of 1-1 against León, the second leg of the match went on to extra time where León goalkeeper Ángel Comizzo shoved and kicked Cruz Azul striker Carlos Hermosillo in the face inside the penalty box. The championship was decided by a golden goal penalty kick taken by Hermosillo, who was bleeding profusely, winning the league for Cruz Azul for the eighth time. This title brought an end to Cruz Azul's 17 year long league drought as well as achieving Cruz Azul's second continental treble.
Cruz Azul has been the Primera División champion nine times, trailing Toluca's 10, C.D. Guadalajara's 12, and Club América's 13. Cruz Azul's six titles makes it the second-most successful club in the history of the CONCACAF Champions League, the most prestigious international club competition in North American football, trailing intracity rival Club América. Cruz Azul was also the first CONCACAF team to reach the final of the Copa Libertadores, the most prestigious club competition in South American football (which invited top Liga MX clubs from 1998 to 2017), losing on penalties to Argentine football giants Boca Juniors in 2001. In the 1968–69 season, Cruz Azul was the first CONCACAF club (and third worldwide) to complete a rare Continental Treble, winning the Mexican Primera División championship, the Copa México national tournament, and the CONCACAF Champions League.
In 2001, Cruz Azul was invited to a tournament between select Mexican and Venezuelan teams that would then compete in the Copa Libertadores, a tournament of the best South American teams. The two best teams of this qualifying tournament earned immediate placement on the roster.
After leaving a pre-season practice session on July 16, 2005, then manager Rubén Omar Romano was abducted by 5 men after being cornered by two stolen vehicles. A ransom note was later found demanding of Romano's family $500,000. Assistant coach Isaac Mizrahi managed the team during Romano's absence. After 65 days, Romano was rescued and found unharmed after federal agents raided a house in a poor neighborhood where Romano and his kidnappers were thought to be situated. The agents arrested 7 conspirators who were under the orders of convicted abductor Jose Luis Canchola.
In the quarterfinals, Cruz Azul defeated Pumas UNAM with an aggregate score of 3-1. They moved to the semifinals against the Atlante, the first leg was played in Mexico City, and Cruz Azul won 3–1. In the second leg, Cruz Azul and the Atlante played a regular match in Cancún, Quintana Roo, that ended 1–1, resulting in Cruz Azul reaching the Final for the second consecutive time in 2008. In the final, Cruz Azul played against Toluca, both teams tied on winning Mexican titles (at that time with 8 each). The first leg played in Mexico City, and ended with a dramatic 0–2 with a victory for visitors, Toluca, and in the second leg, which was played at "Estadio Nemesio Díez". Cruz Azul won 0–2, making the tie on aggregate "2–2", as the match was tied, they played "extra time" and the draw continued until going to the "Penalty – Shoot out", where Toluca won 7–6 over Cruz Azul, Alejandro Vela was Cruz Azul "villain" because he failed the last "penalty shoot-out", another incident before the match went to "extra time", was a clear foul suffered by Villaluz on the Goal area, Toluca's player "Jose Manuel Cruz Alta" crashed with Cruz Azul player, making him unconscious, but the referee didn't mark the foul even though Cruz Azul player was knocked out, he didn't even take a red card on the Toluca player, (unfortunately Cruz Azul had made his 3 substitutions, so they ended the match playing with only 10 players, an unfair situation, that interfered directly on the final result of the match) this made the Toluca team champions after winning their 9th Mexican title, becoming the 3rd most successful of Mexican title winning teams.
In April 2012, Cruz Azul changed their official name from Club Deportivo, Social y Cultural Cruz Azul, A.C. to simply Cruz Azul Fútbol Club, A.C.
On April 23, 2014, after defeating Toluca, Cruz Azul won their 6th CONCACAF championship, a record at the time. This gave Cruz Azul a berth at the 2014 FIFA Club World Cup, where they would earn a fourth-place finish.
Since the Apertura 2014, Cruz Azul has been unable to qualify to the liguilla playoffs for six consecutive tournaments. Cruz Azul qualified for the liguilla for the first time in three years in the Apertura 2017 season. However, they were eliminated in the quarterfinals by the América, who advanced as the higher-ranked seed, with an aggregate score of 0–0. On 27 November 2017, Cruz Azul announced that Paco Jémez would not renew his contract for the following season.
In the Liga MX Clausura 2018 tournament, Cruz Azul ended up ranked 12th and failed to qualify for the liguilla. Cruz Azul were last place in the group stage of the Clausura 2018 Copa MX. On 7 May 2018, the club announced director of football Eduardo de la Torre's contract had ended and would be replaced by Ricardo Peláez, former director of football for the América.
Cruz Azul faced the Club América in a rematch of the Clausura 2013 final for the Apertura 2018 final. The first leg was played on 13 December 2018 which ended in a scoreless draw. The second leg was played on 16 December 2018 and ended in a 2–0 victory for the Club América. With this defeat, Cruz Azul extended its 21-year-old championship drought in the league for at least another season.
In May 2020, Guillermo "Billy" Alvarez Cuevas, then president of the club, was indicted by Mexican authorities on multiple accounts of insurance fraud, racketeering, extortion, tax evasion, and money laundering. On July 26, an arrest warrant was issued for Alvarez along with board directors Victor Manuel Garcés, Miguel Eduardo Borrell, and Mario Sánchez Álvarez for alleged ties to organized crime. Alvarez subsequently resigned from his position at the club in August 2020 after 32 years as acting president. Interpol is currently searching for Alvarez in 195 countries and as of June 2, 2021, remains at large.
On December 6, 2020, Cruz Azul faced UNAM on the second semi-final leg of the Guardianes 2020 Liga MX final phase. Although Cruz Azul had a 4–0 lead at the beginning of the second leg matchup, they lost the match 0–4, thus tied with UNAM in the final aggregate. However, as UNAM won in week 17 match at 1-0 they held the tie breaker, they advanced to the final.
On May 30, 2021, Cruz Azul ended its 23 year Primera División championship drought by beating Santos Laguna 2-1 on aggregate at Estadio Azteca, earning its ninth league championship.
The club became infamous in Mexico for not having won a Mexican league title from 1997 to 2021. For an English-speaking audience, the so-called "Cruz Azul curse" is likened to Neverkusen for German team Bayer Leverkusen, the Curse of the Bambino for MLB baseball's Boston Red Sox, or the Curse of the Billy Goat for MLB's Chicago Cubs. The commonality derives from these teams' inability, no matter the quality of the team relative to their opponents in a tournament or a championship match, to win a championship. The "curse" was broken after their winning of the Guardianes 2021 final match versus Santos Laguna, after scoring 2-1 on May 30, 2021.