As a player, Aguirre was a member of the Mexico national team and later became coach on two separate occasions, but resigned after the 2010 FIFA World Cup.
Aguirre began his career as a youth product of Club América in 1979, though he was sold to Los Angeles Aztecs of the North American Soccer League. Club América later bought him back, where he established himself as a midfielder. He played an integral part in their various title winning seasons, most notably during the 1983–84 season where América reached the league finals against arch-rivals Guadalajara, managing to score a goal in a 3–1 win at the Estadio Azteca. Aguirre also played outside Mexico, signing with Osasuna in Spain in 1986. In 1987, he transferred to Guadalajara, where he made over 100 appearances up until his retirement in 1993.
Aguirre made 59 appearances for the Mexico national team between 1983 and 1992, scoring 13 goals. He played in the FIFA World Cup in 1986, and was sent off in the quarter-final defeat to West Germany.
After retiring as a player, he took up managing, first with Atlante and then Club Pachuca, where he won the Invierno championship in 1999.
In 2001, he replaced Enrique Meza as the manager of Mexico due to poor results. That same year, he managed them in the 2001 Copa América, but lost 0–1 in the final against host nation Colombia. In 2002, he managed them in the 2002 FIFA World Cup. Mexico, commanded by Aguirre, were placed in Group G with Croatia, Italy, and Ecuador. Mexico were later eliminated from the World Cup, after losing 0–2 to the United States in the second round.
Aguirre was then hired to coach CA Osasuna replacing Miguel Angel Lotina departed to Celta de Vigo, club for which he played for, of the Spanish La Liga, where he has been one of the most consistent coaches in the past years, mostly due to the achievement of all the goals he sets. After being hired to save Osasuna in 2002, he did so and stayed with the team until 2006, when he earned them a spot in the Champions League 3rd Qualifying Phase after a fourth-place finish during the 2005–06 season, culminating in entry to the UEFA Cup.
The overwhelming success Aguirre achieved with a small budgeted team earned him the spot on Atlético Madrid's bench. In the first season (2006–07), his task was to get the team back in a European competition and he did so by putting Atlético in the UEFA Cup. The second year's goal (2007–08) was a more ambitious one: the Champions League. After an irregular season, Atlético earned a ticket to the 2008–09 UEFA Champions League under Aguirre's command.
On 2 February, Spanish sports newspaper Marca reported that Aguirre would be replaced by ex-Atlético goalkeeper and CD Castellón manager Abel Resino. The club cited Atlético's recently lacking performance in the new year as reasons for Aguirre's dismissal (Atlético had not won a single game in 2009, up to that point). While most of the club felt his dismissal was necessary, some see his departure as unfair since Aguirre elevated the club to a level it had not seen in almost 14 years.
On 3 April 2009, Aguirre was officially appointed as the new manager of the Mexico national team after the poor performance of Sven-Göran Eriksson. Many believe that Eriksson was the scapegoat to be blamed because of Mexico's recently weak team, but brought average results for Mexico. He was officially presented as Mexico manager in a press conference on 16 April 2009. At the press conference, he stated: "I add, gentlemen, that I want the player who comes, come with pride, to recover the identity that comes with our love for the shirt" and that a call-up "is a reward and not a punishment, that we're all here because it is a prize for our careers." His annual salary was US$1,635,000.
On 6 June 2009, Aguirre debuted in a 2010 FIFA World Cup qualifier against El Salvador, losing 2–1. However, he rebounded four days later with a 2–1 win over Trinidad and Tobago.
On 9 July 2009, Aguirre was ejected in an incident during the 2009 CONCACAF Gold Cup match versus Panama. During a play along the sideline, Aguirre kicked Panamanian player Ricardo Phillips, triggering Phillips to push Aguirre, causing ejections for both Aguirre and Phillips and delaying the match for over 10 minutes due the refusal of the player from Panama to leave the field. Aguirre apologized to the Mexican fans, media, football players and staff, but never extended such courtesy to Philips or the Panamanian team. He was suspended for three games and the Mexican Football Federation was fined USD $25,000 by CONCACAF.
On 26 July 2009, Aguirre led Mexico to its fifth Gold Cup title and its first win against the United States outside of Mexico since 1999. He then led Mexico to a comeback win over the same opposition at the Estadio Azteca on 12 August 2009 and followed it up by winning 3–0 in Costa Rica, putting Mexico closer to a qualifying spot for the World Cup that seemed to be an impossible task at the time when Eriksson was sacked. On 10 October 2009, Mexico beat El Salvador in the Estadio Azteca 4–1, qualifying Mexico for the 2010 FIFA World Cup.
After that, in their last hexagonal game against Trinidad and Tobago, they tied 2-2, ending the World Cup qualifying journey.
On 30 June 2010, Aguirre resigned as coach of Mexico following their failure to reach the quarter-finals of the 2010 FIFA World Cup in South Africa. Mexico finished second in Group A, ahead of hosts South Africa and France, but their progress was halted in the second round where they were defeated 3–1 by Argentina.
Aguirre was named manager of Real Zaragoza on 17 November 2010, he was presented in a press conference the following day. He was sacked on 29 December 2011 for putting the team in the relegation zone, the club owner quoted that the team has never done so bad in their club history .
On 28 November 2012, Aguirre was named manager of RCD Espanyol, at that point 20th in the La Liga table. He kept them up in the 2013–14 season by three points. Aguirre announced he was leaving Espanyol on 16 May 2014, and was replaced 11 days later by former player Sergio.
In August 2014, Aguirre was named as new manager of the Japan national team, replacing Alberto Zaccheroni, who had resigned following the World Cup. At the 2015 AFC Asian Cup, Japan won all three of its group matches, scoring seven goals and conceding none, though was knocked out in the quarter final by the United Arab Emirates.
On 3 February 2015, the Japanese Football Association announced they had annulled the contract with Aguirre, after they confirmed that Spanish anti-corruption investigators had indicted Aguirre, who they alleged was involved in an ongoing match-fixing investigation over Real Zaragoza's 2–1 win over Levante on the final day of the 2010–11 season, while Aguirre was manager of Zaragoza.
On June 18, 2015, Aguirre was hired as new manager of the Al-Wahda FC from United Arab Emirates. On May 21, 2017, after leading Al Wahda to the President's Cup championship victory, Aguirre decided to step down as manager.
Aguirre's decision-making during the qualifying stages and especially during the World Cup grew increasingly controversial, with the ESPN broadcaster José Ramón Fernández calling him the worst coach in the World Cup after France's Raymond Domenech. In particular, his insistence on playing team-less striker Guillermo Franco while keeping Manchester United striker Javier Hernández on the bench bewildered many fans and commentators. The 33-year-old Franco played poorly and failed to score a goal, while the 22-year-old Hernández scored two goals, once off the bench in the 2–0 victory over France and another as a starter in the 3–1 second-round loss to Argentina.
Aguirre came under criticism for his refusal to explain his personnel decisions. This has led to the proliferation of rumors in Mexico concerning Aguirre's and others' various ulterior motives. These rumors referenced the financial interests of the two major Mexican TV stations, Televisa and TV Azteca, as well as those of various soccer promoters and of the owners of Mexico's first-division teams, all of which wield enormous influence over the Mexico national team. Another questionable topic for Aguirre was the role played by Aguirre's assistant Mario Carrillo, who was supposedly in charge of Mexico's tactical work, but whose real role was never fully explained to the public. During the run up to the World Cup Aguirre expressed his desire to coach in the Premier League in England but received no offers.
In January 2015, it has been reported by Spanish media that a Valencia court has accepted a claim filed by Spanish prosecutors alleging some 40 people, including Aguirre, were involved in fixing a match between his former club Real Zaragoza and Levante UD in 2011, followed by court proceedings expected to start in February, when Aguirre could be asked to appear in court to defend himself, although he denied the accusations at the press conference held in December 2014.As of 23 December 2016
Mexican Primera División: 1983–84
Mexican Primera División: Invierno 1999
UAE President's Cup: 2016–17
UAE League Cup: 2015–16
CONCACAF Gold Cup: 2009