Born in Leones, Córdoba, Pellegrino played for Club Atlético Vélez Sarsfield during a large portion of the 90s, as the Buenos Aires-based club experienced its golden age, winning four Primeira División championships and the 1994Intercontinental and Libertadores Cups. He had his first experience abroad in 1998–99, joining Louis van Gaal's FC Barcelonaon loan. He made his La Liga debut on 12 September 1998 in a 1–0 home win against CF Extremadura, and would be used regularly during the campaign, which ended with league conquest.
Valencia
Pellegrino had his best years with another Spanish side, Valencia CF, partnering countryman Roberto Ayala in the heart of the back-four while helping them to two league titles during his tenure, with the addition of the 2003–04 edition of the UEFA Cup. Arguably his worst moment occurred during the 2000–01final of the UEFA Champions League as he missed the last penalty shootout attempt against FC Bayern Munich – he also played in the previous season's decisive match, which also ended in defeat, to Real Madrid. Overall though, in his six years at the Mestalla Stadium, he was a very important defensive unit, and amassed 213 official appearances for the Che.
Liverpool / Retirement
In early January 2005, after having been frozen out by Claudio Ranieri, Pellegrino joined former Valencia boss Rafael Benítez at Liverpool on a free transfer, signing a six-month contract– this move made him the first Argentine player in the history of the club. He played 12 times for the Reds in the Premier League – 13 overall – but his performances were not enough to secure a longer contract, and he was released by the club at the end of the season. He was cup-tied for the Champions League campaign, and did not feature in the victory over A.C. Milan in the final of the competition. Afterwards, Pellegrino returned to Spain, having an unassuming stint with Deportivo Alavés.
International
Pellegrino earned three caps for Argentina, all during 1997. He was picked for the squad at that year's Copa América and made his debut in the continental tournament against Ecuador in the group stage.
Coaching career
After retiring in June 2006, Pellegrino stayed connected with Valencia, coaching its Cadete-B. Two years later he decided to return to Liverpool, who still had Benítez in charge, as first-team coach, a position in which he remained until the middle of 2010 as the pair moved to Inter Milan. In December 2010, as Benítez resigned from his post, Pellegrino was also dismissed. On 7 May 2012 he was appointed at former club Valencia, signing for two years as a replacement for Unai Emery who left at the end of the season. On 1 December 2012, following a 2–5 home loss against Real Sociedad which left the side in 12th place, Pellegrino was relieved of his duties. He subsequently returned to his country, signing with Estudiantes de La Plata. On 14 April 2015, Pellegrino was sacked by president Juan Sebastián Verón. In June, he was appointed at fellow league team Club Atlético Independiente. Pellegrino returned to Alavés on 26 June 2016, being named José Bordalás's successor as the club had just been promoted to the top flight. In his first season he qualified the team for the final of the Copa del Reyfor the first time ever, after a 1–0 aggregate defeat of RC Celta de Vigo; in the decisive match, played in Madrid, they lost 3–1 to Barcelona. On 23 June 2017, Pellegrino was appointed manager of Southampton on a three-year contract. He was dismissed the following 12 March, with the team at risk of relegation after winning one of their last 17 matches. Pellegrino returned to the Spanish top division on 2 June 2018, signing a one-year deal with CD Leganés. In October 2019, as the side was last in the standings with only two points, he left by mutual consent. On 16 April 2020, Pellegrino replaced Gabriel Heinze at the helm of Vélez Sarsfield and agreed to a contract until June 2021.