Márquez began his career with Atlas, for whom he debuted in October 1996 at only 17 years of age. Márquez rose to prominence while with Atlas, making 77 appearances for the team and being runner-up in the league, losing the final against Toluca on penalties during the Verano 1999 tournament.

Márquez made his debut with Mexico on 5 February 1997 in a friendly match against Ecuador. It was reported that his call-up was due to an error made by national team coach Bora Milutinović, who wanted to call up fellow Atlas player César Márquez. Márquez became a regular call-up for Mexico, although he was not chosen for the 1998 FIFA World Cup squad. Márquez played various tournaments with the Mexican team, winning the 1999 FIFA Confederations Cup and losing to Canada at the 2000 CONCACAF Gold Cup. Márquez started all four of Mexico’s games during the 2002 World Cup in South Korea and Japan, where he was given the captain’s armband by then coach Javier Aguirre despite his young age of 23. He received a red card during Mexico’s second round 2–0 loss to the United States for a deliberate mid-air head butt on Cobi Jones in the final minutes of the match.

Márquez’s father, Rafael Márquez Esqueda, was also a professional football player in Mexico. Rafael married Mexican actress Adriana Lavat in December 2001 and had two children, Santiago Rafael and Rafaela, before separating in 2007 and divorcing. He is now married to Jaydy Michel, ex-wife of singer Alejandro Sanz. His younger cousin, Luis Márquez, is also a professional footballer. Luis was formed in Atlas’ rival club, Guadalajara and currently plays on loan at Zacatepec.

In the summer of 2003, Márquez signed for Spanish club FC Barcelona. He made his debut in La Liga on 3 September 2003 against Sevilla, the match ending in a 1–1 draw. On 9 November, he scored his first goal for Barcelona in their 2–1 victory over Real Betis. In his first season with Barcelona, Márquez made 22 league appearances (31 across all competitions) as the team finished second in the league, five points behind Valencia.

During his second season, he was moved from his natural position as a centre back to a defensive midfield role, due to injuries to players Thiago Motta, Edmílson and Gerard. That year, Barcelona won its 17th league title on 14 May 2005 after a 1–1 tie with Levante. A month after an injury to his left knee, Márquez returned to play against Milan in the first leg of the 2006 UEFA Champions League semi-final. Barcelona, playing away at the San Siro, won 1–0. On 17 May, Barcelona won the UEFA Champions League after defeating Arsenal 2–1 in the final, with Márquez playing the entire match. He became the first Mexican to play in a Champions League final and the first to win it. Following his participation with Mexico at the 2006 World Cup, Márquez signed a four-year contract extension with Barcelona, with the buy-out clause set at €100 million.

During the 2007–08 season, Márquez formed a partnership with new signing Gabriel Milito while captain Carles Puyol was out injured. Constant injuries, however, threw off his form. Márquez’s success declined with the rest of the season, leading Barcelona to end up in third place in La Liga after a miserable second half where injuries lead to his contribution being negligible. Even so, new coach Pep Guardiola continued to rely on his contributions; with the departure of Ronaldinho, Márquez had become the last original signing of the Frank Rijkaard era to remain on the team. In October 2007, Márquez was included in the list of players nominated for the FIFA World Player of the Year award, the only player from the CONCACAF to be nominated.

New Mexico coach Hugo Sánchez called-up Márquez to participate in the 2007 CONCACAF Gold Cup and the 2007 Copa América. Márquez joined up with the team Mexico for the Gold Cup’s championship game against the United States after the conclusion of 2006–07 La Liga; he started the match, which Mexico lost 2–1.

Márquez was Guardiola’s first-choice at centre back along with captain Puyol for the 2008–09 season. On 13 December 2008, Márquez played his 200th match for Barcelona in their 2–0 win against Real Madrid. On 28 April 2009, during Barcelona’s 2008–09 Champions League semi-final match against Chelsea, Márquez sustained a knee injury which required surgery, meaning he would miss the remainder of the season. Barcelona would go on to complete a historic treble after winning the Champions League final against Manchester United.

Prior to the 2009–10 season, Márquez received an offer from Italian Serie A club Fiorentina. Márquez, however, said he wanted to end his career at Barcelona. Márquez eventually signed a new contract with Barça in November 2009 that would keep him at the club until 2012. On 20 February 2010, he scored his first goal since his return against Racing Santander.

On 31 July 2010, Márquez was released from his contract by Barcelona. During his time with the club, he played in 242 matches and scored 13 goals, making him the most-capped non-European player in the club’s history and the eighth-most capped foreigner. In his 12-year European career, Márquez appeared in 46 UEFA Champions League matches, which was the most by a Mexican or CONCACAF player, until compatriot Javier Hernández surpassed that record in 2017. At the time, Márquez was also one of two players from CONCACAF to play in a Champions League final, the other being Trinidad and Tobago’s Dwight Yorke.

On 1 August 2010, it was announced that Márquez had signed with the New York Red Bulls of Major League Soccer on a three-and-a-half-year contract. He was the club’s third Designated Player and was unveiled to the media at Red Bull Arena on 3 August wearing the number 4 jersey and reuniting with former Barcelona teammate Thierry Henry. On 8 August, Márquez made his MLS debut against the Chicago Fire in a scoreless draw. On 21 August, Márquez scored his first goal, an astonishing shot with his right foot, for the Red Bulls in a 4–1 win at Toronto FC. On 21 October, Márquez started for the Red Bulls in a 2–0 victory over New England Revolution which clinched the regular season Eastern Conference title.

On 29 March 2011, Márquez became the eighth player in history to reach 100 caps for Mexico in a friendly match against Venezuela, where Mexico drew 1–1.

New York released Márquez on 13 December 2012. His stint in New York was heavily criticized by many fans and journalists for his constant injuries, suspensions and perceived lack of commitment to the fans and club. Márquez later revealed in an interview with ESPN Deportes that going to play in the United States was “a bad decision” and called it the worst decision he ever made in his career. He said that he had misjudged the arc of his career, believing it was declining faster than it was, and that he regretted declining offers from various European clubs, including one from Italian side Juventus.

On 7 August 2014, Hellas Verona of Serie A signed Márquez on undisclosed terms. He stated that he had taken a pay cut to join the club as he was desperate to return to Europe. He made his debut in the league on 31 August, starting as Verona played out a goalless draw at home against Atalanta.

On 21 December 2015, it was announced that Márquez had officially transferred to Atlas, returning to the club he debuted with. He was handed the number 4 shirt.

In May 2015, it was announced Márquez was included in the 23-man squad that would participate in the Copa América tournament in Chile. He was selected to start as captain in Mexico’s opening fixture of the tournament, a 0–0 draw with Bolivia in Viña del Mar. The following year, Márquez captained Mexico at the Copa América Centenario, scoring in their opening game a 3–1 victory over Uruguay.

On 11 November 2016, in a 2018 World Cup qualifier in Columbus, Ohio, Márquez scored the winning goal for Mexico in the 89th minute to seal a 2–1 victory over the United States.

On 9 August 2017, it was reported that Márquez was among 22 people sanctioned under the Foreign Narcotics Kingpin Designation Act (also known as the “Kingpin Act”) by the United States Treasury Department for alleged ties to a drug trafficking organization allegedly headed by Raúl Flores Hernández, a suspected drug trafficker with links to the Sinaloa Cartel and the Jalisco New Generation Cartel. He was placed on a Specially Designated Nationals List by the Treasury Department’s Office of Foreign Assets Control (OFAC). Nine businesses, including a soccer school and charitable foundation, were linked to Márquez by the OFAC. All 22 people were accused of providing support to, or being under the control of Flores Hernández.

On 19 April 2018, Márquez announced that he would retire at the end of the season. He did, however, state his intention of representing Mexico at the World Cup. Márquez played his final match at the Estadio Jalisco on 20 April, a 1–0 victory in the Clásico Tapatío against Guadalajara. The following week, Márquez played his final club match against Pachuca at the Estadio Hidalgo, which ended in a 0–0 draw.

On 4 June 2018, Marquez was named in Mexico’s final 23-man squad for the World Cup. This meant he would travel to his fifth World Cup finals, becoming only the fourth player in history to do so, alongside German Lothar Matthäus, Italian Gianluigi Buffon and fellow Mexican Antonio Carbajal. He was substituted in for Andrés Guardado at the 74th minute in Mexico’s 1–0 win over defending-champions Germany, and became the third man in history to play at a fifth World Cup. On 2 July, in Mexico’s round of 16 match against Brazil, Márquez became the first player ever to play as a captain in five World Cups and was substituted off at half-time, marking his last appearance as a professional.