He made his name playing for Tigres UANL, where he had his most success.
He played for Santiago Wanderers and for Universidad Católica, and arrived to Monterrey, Mexico to play with Tigres in 1996. Tigres had just been privatized after a crisis that ended with the team's relegation to Primera División A.
His incredible number of goals in Tigres quickly made him a team hero. He was instrumental in returning Tigres to the First Division.
He played 10 seasons with Tigres, 8 in First Division, in which he scored over 40 goals.
He played many Clásico Regiomontano matches, against Tigres arch-rival Rayados de Monterrey. He became the maximum scorer in the history of Tigres for these kind of matches, with eight goals. His record was tied by Walter Gaitán in January 2007.
An injury separated him from the fields, and Tigres consequently separated him from the team in 2001. In 2002 he moved to play with Puebla F.C., a team that has been relegated to Primera División A.
He used to wear the number 16 on his back for every match he played.
In 2005 he played his first Copa Libertadores de América with Tigres, where he scored some goals.
Nuñez has also played for Unión Española in Chile and Al-Shoalah in Saudi Arabia.
For his country Nuñez played 31 matches scoring 4 goals between 1996 and 2003.
A farewell Clásico Regiomontano match where Nuñez will play with special guests from Tigres and Monterrey is scheduled for August 4, 2009 at the Estadio Universitario, Tigres' home stadium.