Named team president on July 17, 2013, Dee spent 10 years total with San Diego over two stays. During his tenure as CEO, the Padres hired current general manager A.J. Preller and manager Andy Green.
It is unclear who will succeed Dee, but Fowler told the San Diego Union-Tribune that "the search will begin immediately."
In 2014, Dee and the Padres dismissed GM Josh Byrnes, before ultimately naming Preller his successor that summer. Preller is currently serving a 30-day suspension for undisclosed medical information in the Padres' trade of Drew Pomeranz to the Red Sox in July.