Stammen spent 13 seasons as a pitcher, including six with the Padres from 2017-2022, and will now be in his first MLB managerial role.
He remained with the Padres as an assistant on the coaching staff, but has never held the top managerial role at any level of the game.
He'll take over the job vacated in October by Mike Shildt, who cited the "grind of the baseball season" when he stepped down for personal reasons (read more here).
Shildt led the Padres to back-to-back playoff appearances, but San Diego fell in winner-take-all playoff games in both 2024 and 2025.
"Craig has been here a long time, and the biggest thing you see with Craig is his belief in the Padres organization and his belief in our players," Padres general manager A.J. Preller said in a statement.
"He possesses deep organizational knowledge and brings natural leadership qualities to the manager's chair," Preller said. "As both a player and in his post-playing career, Craig has displayed an ability to elevate those around him. His strength of character, competitive nature and talent for bringing people together make him the ideal choice to lead the Padres."
Stammen, 41, inked a three-year contract with the Padres, who also interviewed pitching coach Ruben Niebla, superstar slugger Albert Pujols and longtime catcher Nick Hundley in their search for Schildt's replacement.