Stonycreek Township is located approximately at 40.01°N by 78.88°W, about 3mi WSW of Indian Lake, Pennsylvania.
According to the United States Census Bureau, the township has a total area of 61.4 square miles (159.1 km2), of which, 61.2 square miles (158.4 km2) of it is land and 0.3 square miles (0.7 km2) of it (0.44%) is water.