Nunez was spotted by Real in 2001 playing for third division side Las Rozas. He played in the reserve team until 2003-2004 when he managed 16 games for Real Madrid as a utility player in their star-studded team. He scored on his debut for Real on 2 September 2003 against Villareal. A dream come true for the boyhood Real fan. Unfortunately, Real finished empty-handed in the 2003/04 season. Nunez was valued at £1.5 million in Michael Owen's £8.5 million move from Liverpool to Real Madrid. It was an exciting prospect for Nunez who wanted to play more than the odd game. "Even if Owen hadn't signed for Madrid, I already had an offer from Liverpool and I knew that the manager was keen to sign me, which is something to be proud of," Nunez said. The attacking midfielder was one of a quartet of Spanish players signed by Rafa Benítez in his first season as manager; Josemi had already arrived and Xabi Alonso and Luis Garcia soon followed suit. Nunez injured his knee in his first day of training and wasn't ready for action until three months later. He made three starts in a row following his Arsenal debut and got fair crack of the whip, but more often than not failed to impress.Nunez did make history by becoming the only Liverpool player to score his only goal for the club in a major final when he reduced Chelsea's 3-1 lead to one goal in extra-time in the 2005 League Cup final loss. Nunez didn't set the world alight at Liverpool, but he won a treasured Champions League medal. He played the full 90 minutes in the crucial group-stage win over Olympiacos and featured for 60 minutes in the goalless draw against Juventus but had to settle for bench duty in the Istanbul final.

Nunez moved back to Spain in the summer of 2005 to join Celta Vigo, who had just been promoted back to the Spanish first division. After three seasons in Vigo, then in second division, he agreed to join Real Murcia who were relegated from the top-flight in 2007/08. Nunez bought out his contract at Murcia after only one season and joined Cyprus' Apollon Limassol in August 2009. After a couple of years on the Mediterranean island, he returned to the country of his birth to sign for second division Huesca where the 33-year-old made 16 appearances and scored four goals in his first year.

Núñez was a regular starter in the Huesca team in 2012/13 but his club spent much of the season fighting to avoid relegation and eventually went down after the final day results. He then signed a one-year contract with Deportivo de La Coruña, then in Spain's Second Division.  Núñez played in 21 of  Deportivo's 40 leasgue matches as his latest club returned to La Liga by finishing runners-up to the Basque club Sociedad Deportiva Eibar. He remained in the second division however by joining Recreativo Huelva, with whom he was relegated although he has remained there for 2015/16, scoring five goals in 35 games in the Segunda B. Nunez spent two further seasons in Spains third tier with Recreativo, finally calling time on his playing career at the end of the 2017-18 season, aged 39.