Rupert is located at 40°58'44" North, 76°28'28" West (40.978965, -76.474524).
According to the United States Census Bureau, the city has a total area of 0.91 mi2 (2.35 km2). 0.91 mi2 (2.35 km2) of it is land and none of the area is covered by water.
Rupert is located in the Eastern Standard Time (EST) timezone, GMT-05:00. It observes Daylight Saving Time (DST).