The former Lazio star will join the Dutch champion in July and will work alongside Frank de Boer and Dennis Bergkamp as he looks to develop as a coach with the Amsterdam outfit.
The 40-year-old has signed a deal until 2016 with the Dutch champion and will move to the Amsterdam ArenA after his contract with PEC Zwolle ends in July.
The former Manchester United and AC Milan center back admitted that he is looking forward to returning to the Dutch capital where he ended his playing career in 2007, while he hopes to continue to learn from working at one of the biggest sides in Europe.
"It's a new challenge at one of the biggest clubs in the Netherlands," he told the PEC Zwolle website. "I think it's nice to go back there since my playing career ended in Amsterdam.
"Moreover, I will experience how things work in the technical staff at a Dutch club. I hope I therefore continue to develop as a coach."
Stam will work alongside his former Netherlands teammates Frank De Boer and Dennis Bergkamp with the Eredivisie winner, with his focus on the defensive side of the game.