The ex-Lazio star will join the Dutch champions in July and will work alongside Frank de Boer and Dennis Bergkamp as he looks to develop as a coach with the Amsterdam outfitAjax as their assistant coach from the start of next season.
The 40-year-old has signed a deal until 2016 with the Dutch champions and will move to the Amsterdam ArenA after his contract with PEC Zwolle ends in July.
The former Manchester United and AC Milan centre-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 team-mates Frank De Boer and Dennis Bergkamp at the Eredivisie winners, with his focus on the defensive side of the game.