Dee replaces Tom Garfinkel, who resigned this summer after holding the post since 2009.
Dee worked for the Padres from 1995 to 2002 and was part of the front- office group that followed former team president and CEO Larry Lucchino to the Red Sox. For the final three years of his first stint with the Padres, Dee was executive vice president of business affairs.
In 2009, Dee became CEO of the Miami Dolphins and Sun Life Stadium.
“It’s a chance to return to my roots,” Dee told the Miami Herald about rejoining the Padres. “This is a great opportunity to run a team and a facility. It’s a chance to sail a ship I helped construct.”