Villarreal confirmed the appointment on their official website, with Pérez — who turned 38 in January — signing a three-year deal to replace Marcelino García Toral, who chose not to extend his contract after guiding the club to third place in La Liga and Champions League qualification.
Pérez takes over as head coach for only the second time in his career, having begun the role at Rayo Vallecano in February 2024 when he succeeded Francisco Rodríguez mid-season.
He had previously been Andoni Iraola's assistant at Vallecas, and was originally due to follow Iraola to Bournemouth before a work permit issue prevented the move. That circumstance left him in Spain — and ultimately in charge of one of the more remarkable stories in recent Spanish football.
He guided Rayo to eighth place in consecutive La Liga seasons, the best back-to-back finishes in the club's recent history, while also taking the Madrid side to the Conference League final in Leipzig — where they lost 1-0 to Crystal Palace. No Rayo manager in the club's 102-year history had led the team to a European final.
Villarreal's ambition is to go further. They return to the Champions League for the first time since the 2021-22 season, when they famously eliminated Juventus, Bayern Munich and Juventus again before losing to Liverpool in the semi-finals. Pérez will be tasked with matching and building on Marcelino's third-place finish as the club prepare for elite European competition.
His appointment follows the path trodden by Iraola before him — a Rayo coach stepping up to a more prominent La Liga post as reward for work that consistently exceeded expectations.