Pérez is a legend of the Liga MX club, having played for them as a goalkeeper from 1993 to 2008, before going onto become a goalkeeping coach there upon his retirement.
Pérez, who played over 50 times for Mexico, succeeds Carlos López de Silanes as Sporting Director.
He said: "It is a golden opportunity for me... Now I have to give back to the institution with a lot of dedication, with a lot of work, to the fans who are always there, who are very demanding. Being here is a great honour for me."
Cruz Azul have access to TransferRoom through a multi-year, league-wide agreement with Liga MX, which has resulted in a number of successful transfers through the platform for the likes of Club Necaxa and Atlético de San Luis.
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