Montoya was among the first cars out on the triangular 2.5-mile track and was clocked at 51.124 seconds, which translated to 176.043 miles per hour.
Montoya then had to sweat out the rest of the morning as the field tired but failed to knock him out of the top slot for Sunday's Sprint Cup race.
It was the eighth pole of Montoya's career, but his first at Pocono and his first of the season.
"To be honest with you, I'm not sure if I'm more shocked that we're on the pole right now -- with how the last few races have been for us and how our season's been -- or that we're on the pole at Pocono," Montoya said. "This is a place where I normally struggle in qualifying."