The 38-year-old, who was team-mates with Karanka during his one-year stint at the Bernabeu, retired from playing in 2005 after a career which saw him represent Real Betis, Bordeaux and Deportivo La Coruna.
Perez is a former youth international with Spain, winning the under-21 European Championship in 1998 before going on to claim La Liga and Ligue 1 titles with Deportivo and Bordeaux respectively.
Perez admits he is grateful for the opportunity to take up his first coaching role in England and says that his sights are already set on a securing Boro a top-flight return.
"I'm going to England to work with Aitor Karanka at Middlesbrough. Since 2013, Aitor has been working there," he told the Veterans of Real Madrid website.
"The team is in the second division and our goal is to get promotion, but we know how hard it is to move up in competitions in English football.
"I thank Aitor for giving me this opportunity, which I will work with with the utmost enthusiasm and commitment."
After spending three years as assistant in Madrid, Karanka became the Boro boss last November and led them to a 12th-place finish in the Championship.
Although he is yet to bolster his squad this summer, reports have claimed that Real Betis full-back Juanfran could be close to a move to the Riverside Stadium.