Stewart turned in a lap of 171.393 mph on the 2.5-mile circuit and will start out front Sunday in the Sunoco Red Cross Pennsylvania 500. It was the 14th pole of his Sprint Cup career, but he is still looking for his first race victory this season.
The outside spot on the first row went to Juan Pablo Montoya, who won the pole last weekend at the Indianapolis Motor Speedway and led for most of the Brickyard 400 before crashing with less than 15 laps to go.
"Last week was a rough week for the team, but to rebound at a place where we don't run that well, it's nice," Montoya said.
Denny Hamlin, who has won the last two races held at Pocono, qualified third. He was followed by four-time winner Jeff Gordon and Ryan Newman.
The next five qualifiers were Jimmie Johnson, A.J. Allmendinger, Jeff Burton, Jamie McMurray and Mark Martin.
Points leader Kevin Harvick, who has a 184-point advantage over the second-place Gordon, will start 14th.