The 68-year-old Gillick succeeds Ed Wade, who was fired on Oct. 10 after eight years in the post.
For the last two years, Gillick has been a special assistant to Seattle General Manager Bill Bavasi. Before that, he was the Mariners' general manager for four years.
The Phillies hired Gillick over former Houston Astros GM Gerry Hunsicker and Phillies assistant general manager Ruben Amaro Jr.
"I think this is a very good situation," Gillick said.
This past season, Philadelphia finished 88-74, but failed in its bid to clinch the National League wild-card berth on the last day. The Astros earned the spot.
The Phillies have had 80 or more wins in each of the last five seasons but have not gone to the post-season since 1993, when they were beaten by Toronto. Gillick was then the Blue Jays' GM.