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A native of Honduras, Nunez moved to Dallas with his family in the early 1990s where he attended W.T. White High School and, later, SMU. In his freshman season with the Mustangs, Nunez earned Missouri Valley Conference Freshman of the Year honors, before electing to leave college for the professional ranks. FC Dallas, then the Dallas Burn, selected Nunez sixth overall in the 2004 MLS SuperDraft.
While with Dallas, Nunez appeared in 67 games, scoring 14 goals and tallying nine assists. He left FC Dallas in 2007 for Chivas USA, where he appeared in just eight games, tallying three assists. Following the 2007 season with Chivas USA, Nunez returned to Honduras where he joined Olimpia, making 34 appearances and earning player of the season honors following the 2007-08 Clausura. From Olimpia, Nunez joined Mexican First Division side Puebla on a six-month loan, scoring five goals and tallying five assists during the loan spell.
Nunez remained in Mexico following his performance at Puebla, joining Cruz Azul in 2009 for six months before returning to Olimpia in Honduras. When his six-month contract with the Honduran side ended, Nunez traveled across the pond to join English Championship side Leeds United where he made 20 appearances and scored one goal. Nunez spent a brief loan spell with Scunthorpe United in 2011, appearing in eight games and scoring three goals, before returning to Leeds and signing a new contract with the English club. In September 2012, Nunez suffered a torn Anterior Cruciate Ligament and, upon mutually terminating his contract with Leeds, returned home to Dallas in February to train with his original club.
Nunez, who played in the 2010 World Cup for Honduras, has five goals in 44 appearances for his native country.