St. Marys is located at 41°26'15" North, 78°32'33" West (41.437600, -78.542724).
According to the United States Census Bureau, the city has a total area of 99.48 mi2 (257.66 km2). 99.32 mi2 (257.25 km2) of it is land and 0.16 mi2 (0.41 km2) of it is covered by water. The total area is 0.16% water.
St. Marys is located in the Eastern Standard Time (EST) timezone, GMT-05:00. It observes Daylight Saving Time (DST).