Martino played mostly for Newell's Old Boys in his native Rosario. He holds the record of appearances with the team playing a total of 505 matches in all official competitions. He was also selected in a fan's poll as Newell's best player throughout the club's history.

Martino was chosen to replace Tito Vilanova as manager of FC Barcelona at the start of the 2013–14 season, but announced his resignation on 17 May 2014, though his side finished runner-up in both the Copa del Rey and La Liga that season. In 2015, he led Argentina to the Copa América Final, only to be defeated by hosts Chile on penalties. His team also finished as runners-up in the Copa América Centenario, again losing to the defending champion Chile on penalties. On 5 July 2016, Martino resigned from the Argentine national team.

Martino was assigned as head coach of the Paraguayan national football team in February 2007, replacing Uruguayan Anibal "Maño" Ruiz. His knowledge and success while coaching Paraguayan clubs were the parameters that positioned him as the best option for the job (other candidates were Nery Pumpido and Miguel Ángel Russo). Previously, Martino had won the Paraguayan league four times from 2002 till 2006.

In 2008, Martino was linked for vacant managerial position of Iran Pro League side Steel Azin but the deal was cancelled due to personal reasons. On 5 July 2010, Martino announced that he would be stepping down as Paraguay coach on their return from the 2010 FIFA World Cup in which he led Paraguay to quarter-finals. Martino confirmed that with his four-year contract expiring, he would not be extending his spell in charge of the national side. However, on 10 July 2010, Martino agreed to stay on as Paraguay coach until after the 2011 Copa America, in which Paraguay were runners-up after losing to Uruguay in the final.

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