Juan Nunez was born in Madrid and joined Real Madrid's youth ranks in 2015. He was named MVP of the 2019-2020 Euroleague Next Generation Tournament qualifying tournament in Munich, averaging 9.5 points and 5 assists in 4 games. In 2021, Nunez won the Euroleague Next Generation Tournament with Real Madrid. Although he played in group games, he was called up by Pablo Laso to the senior team and missed the final game of tournament. In June of 2021, Nunez made his debut for Real Madrid's senior team in an ACB semifinal win against Valencia Basket, scoring 2 points and adding 2 rebounds and 1 assist in 7 minutes.
In August of 2022, Nunez signed with Ratiopharm Ulm of the German Basketball Bundesliga. He averaged 7.1 points, 4.6 assists and 3.1 rebounds in his debut. This past season Nunez saw his shooting numbers improve. He shot over 50% from the field and averaged 10.4 points per game. Nunez announced his intentions to enter the NBA draft at the end of the season.