Hillsboro is located at 43°39'6" North, 90°20'36" West (43.651944, -90.343611).
According to the United States Census Bureau, the city has a total area of 1.23 mi2 (3.18 km2). 1.20 mi2 (3.10 km2) of it is land and 0.03 mi2 (0.08 km2) of it is covered by water. The total area is 2.42% water.
Hillsboro is located in the Central Standard Time (CST) timezone, GMT-06:00. It observes Daylight Saving Time (DST).