On 1 January 2016, Fernández joined Atlético Madrid on a three-year deal for an undisclosed fee, mainly as a cover to the injured Tiago. He made his debut 5 days later, playing 57 minutes of a Copa del Rey draw away to Rayo Vallecano before being replaced by Luciano Vietto; he made his first league appearance for the club on the 11th of January, against Celta, his former team. Later, he started in the 2016 Champions League final, although he was substituted off at half-time. He only made 8 appearances in the following seasons with the "Rojiblancos".