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 assigned as head coach of the Paraguayan national football team in February 2007, replacing UruguayanAnibal 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. 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.
After reaching Copa Libertadores semifinals with Argentine side Newell's Old Boys, On 22 July 2013, Martino was confirmed as manager of Spanish club FC Barcelona to replace Tito Vilanova who resigned three days earlier. He signed a two-year deal at Barcelona. His first competitive game in charge of Barcelona was on 18 August 2013 against Levante UD, a game which Barcelona won 7-0 on the opening weekend of the 2013–14 La Liga season. On 26 October 2013, Martino won 2-1 against rivals Real Madrid at the Camp Nou, winning his first Clasico as a Barcelona Coach. Three days later Barcelona went on to win 3-0 at Celta and Martino became the first coach in Barcelona history to not lose their first 16 matches. On 26th November 2013, Martino's unbeaten start as Barcelona coach came to an end after his 21st game in charge, as Barcelona lost 2-1 away at Ajax in the 2013-14 UEFA Champions League.