On 25 August 2017, Núñez received his first call-up to the Spain under-21 squad. He was called up to the full side by manager Robert Moreno on 30 August 2019, for two UEFA Euro 2020 qualifying matches against Romania and the Faroe Islands. He made his debut in the second fixture in Gijon on 8 September, coming on as a late substitute for Sergio Ramos with Spain 2–0 ahead; the final result was 4–0.
