In December 1943, R. R. M. Carpenter Jr., the new owner of the Philadelphia Phillies, hired Pennock as his general manager, after receiving a recommendation from Mack. Carpenter gave Pennock a lifetime contract. Pennock filled Carpenter's duties when the team's owner was drafted into service during World War II in 1944. As general manager, Pennock changed the team's name to the "Blue Jays"—a temporary measure abandoned after the season—and invested $1 million ($ in current dollar terms) into players who would become known as the "Whiz Kids", who won the National League pennant in 1950, including Curt Simmons and Willie Jones. He also created a "Grandstand Managers Club", the first in baseball history, allowing fans to give feedback to the team, and advocated for the repeal of the Bonus Rule.