Born in Río Cuarto, Córdoba, Aimar’s football career begun in earnest when he was offered the chance to play for Estudiantes de Río Cuarto by youth coach Alfie Mercado. He trained with the club’s academy three times a week and it was there that he was spotted by River Plate who offered the chance to join their own academy. Aimar’s father initially prevented him from joining River as he felt he was too young to be playing football, but relented after manager Daniel Passarella personally asked him to allow his son to play. Having turned down the opportunity to attend medical school to pursue a career in football, Aimar made his debut for River on 11 August 1996 against Colón. His first goal for the club came on 20 February 1998 against Rosario Central. Aimar lifted five titles with River between 1996 and 2000, scoring 21 goals and recording 28 assists in 82 league appearances for the club, with his final appearance coming on 17 December 2000 in a 3–2 loss to Lanús.

Aimar first represented Argentina at youth levels. Along with future senior team players Esteban Cambiasso and Juan Román Riquelme he won the 1997 FIFA World Youth Championship and went on to earn 52 senior caps following his debut in 1999, scoring eight international goals in total. He represented Argentina at the 1999 and 2007 editions of the Copa América, at the 2002 and 2006 FIFA World Cups, and at the 2005 FIFA Confederations Cup.

In January 2001, Spanish La Liga side Valencia signed Aimar from River for a club-record fee of €24 million (£13 million). He made his debut for the club the following month against Manchester United and drew praise from three-time Ballon d’Or winner Johan Cruyff for his performance after the match. The following weekend he scored on his La Liga debut, netting in a 2–0 away win over Las Palmas. Aimar immediately became a key figure in Valencia’s midfield under Héctor Cúper and helped the club reach the 2001 UEFA Champions League final, where they lost to Bayern Munich on penalties.

In the 2002 World Cup, for which he was picked ahead of Riquelme, Aimar appeared against England, subbing in for Juan Sebastián Verón in the 1–0 loss, which led coach Marcelo Bielsa to start him against Sweden at the latter’s expense.

An elegant, technically gifted, and creative attacking midfielder, with a small frame, Aimar was a right-footed player, with vast array of skills and an eye for goal. He excelled in a free role as an advanced playmaker, where he was best able to utilise his dribbling skills, vision, and passing ability to create chances for team-mates and orchestrate attacking moves. His skills and playing style saw him earn comparisons with Diego Maradona in his youth. Due to his talent and flamboyance, he was given the nicknames El Payaso (the clown) and El Mago (the wizard) throughout his career. As a youth, compatriot Lionel Messi stated in 2002 that Aimar was one of his biggest influences as a player. In addition to his playing ability, Aimar also drew praise for his leadership qualities; however, despite his talent, he struggled with injuries throughout his career.

Aimar scored the last goal of the 2005 FIFA Confederations Cup during Argentina’s 4–1 loss in the final to champions Brazil. He also appeared with the national side in the 2007 Copa América, scoring a goal in a 4–1 win against the United States in his team’s opening group match of the competition; Argentina went on to reach the final of the tournament, losing out to Brazil once again, this time 0–3, with Aimar coming on as a second-half substitute for Cambiasso.

On 17 July 2008, Aimar signed a four-year contract with Portuguese side Benfica for a fee of €6.5 million. After struggling with injuries initially, he finished the campaign with a string of strong performances and was able to add a Taça da Liga title to his name.

After several months in the sidelines, Aimar received another international callup in October 2009, for decisive 2010 World Cup qualifiers against Peru and Uruguay. In the match against the former he repaid the faith placed in him by coach Diego Maradona, assisting Gonzalo Higuaín for Argentina’s opener with a through ball, in an eventual 2–1 win.

Aimar had become a fan favourite at the Estádio da Luz but injuries continued to plague him, and his game time reduced in the coming seasons. In spite of this, he helped the club to its third and fourth consecutive Taça da Liga titles. On 6 June 2013, after 179 official appearances, 17 goals and 34 assists, Aimar announced he was leaving Benfica and thanked the club for “five wonderful years”.

On 7 August 2013, Tunku Ismail Ibrahim, the president of Malaysian club Johor Darul Ta’zim, confirmed that Aimar had signed a two-year contract with the team. Upon arrival, he became the highest paid player ever to feature in the Malaysia Super League. He made his debut in the league six months after signing, in a 2–0 win against Perak FA. Prior to making his debut, Aimar had previously played at the Larkin Stadium, home of Johor, before with Argentina in the 1997 Youth World Cup. He ultimately made 8 appearances for the club and scored two goals before a spate of injuries resulted in him being released on 21 April 2014. Aimar did earn a champions medal for his time with JDT, though, as the club went on to lift the Super League title at the end of the season.

On 5 January 2015, Aimar returned to River Plate for the club’s pre-season training, stating that he would sign with the club only if he could deal with the physical demand after having undergone surgeries to his heel and not having played since leaving Johor Darul in April 2014. On 31 May, he played as substitute in a home win against Rosario Central in the Primera División. Aimar announced his retirement on 14 July 2015 after River Plate coach Marcelo Gallardo informed him that he was not included in the club’s squad for the semi-final stage of the Copa Libertadores. Gallardo said Aimar was “suffering” and had struggled with injuries through the pre-season.

Aimar was appointed as coach of the Argentina national under-17 football team in July 2017. His under-17 team won the South American U-17 Championship in 2019.

On 16 January 2018, Aimar played in a friendly match for his youth club Estudiantes de Río Cuarto. After the match, he announced that he would be joining the squad ahead of the Copa Argentina fixture against Sportivo Belgrano on 23 January, in order to fulfill his wish of making an official appearance for the club where he began and spent eight years.