Born in Madrid, Núñez started his career with CD San Federico, before joining Tercera División team CD Las Rozas. In 2001 he moved to Real Madrid, his favourite club growing up. Courtesy of manager Carlos Queiroz, Núñez was promoted to the main squad for the 2003–04 season. On 2 September 2003, in his La Liga debut, he came on as a substitute for Javier Portillo 15 minutes from time in an away game against Villarreal CF and scored the 1–1 equalizer after just seven minutes; during the remainder of the campaign, however, in which the Merengues came up totally empty, he only amassed a further ten league appearances, all from the bench.
Liverpool
In August 2004, Núñez was transferred to Liverpool, becoming Rafael Benítez's second signing as club manager – after compatriot Josemi – as part of an exchange deal that saw Michael Owen go in the opposite direction for £8 million. He injured his knee in his first day of training for his new club, and was out of action for three months; he made his Reds debut as a starter in a Premier League match against Portsmouth, a 1–1 home draw on 14 December. Núñez scored his first and only goal for Liverpool in the 2–3 loss against Chelsea for the Football League Cupfinal, therefore becoming the only player in the club's history to score his only goal for the team in a major cup final. In his only season, he also won a UEFA Champions League medal, as he was one of the substitutes in the final against A.C. Milan, appearing in five matches during the campaign, four as a substitute.
Celta / Later years
Following a disappointing season, Núñez transferred back to Spain and joined newly promotedRC Celta de Vigo on 26 July 2005. During his three-year spell with the Galicians, where he would be heavily played, he also lived one top flight relegation, and joined Real Murciain the summer of 2008. In August 2009, Núñez bought out the remainder of his Murcia contract and was released, shortly after joining Cyprus' Apollon Limassol. After three seasons he returned to his country and its Segunda División, signing a one-and-a-half-year deal with SD Huesca. After the team's relegation in 2013, he remained in the division by agreeing to a four-month contract at Deportivo de La Coruña on 12 September; he was part of the squad that returned to the top flight after one year, but started in only seven matches and did not score once. On 8 July 2014, Núñez signed a one-year deal at Recreativo de Huelva, scoring five times in his first season as the team descended to Segunda División B. In April 2016, he spoke to Diario AS about the club's financial emergency that was threatening its existence.
