Marathon City is located at 44°55'47" North, 89°50'22" West (44.929882, -89.839524).
According to the United States Census Bureau, the city has a total area of 2.04 mi2 (5.29 km2). 2.04 mi2 (5.27 km2) of it is land and 0.01 mi2 (0.02 km2) of it is covered by water. The total area is 0.39% water.
Marathon City is located in the Central Standard Time (CST) timezone, GMT-06:00. It observes Daylight Saving Time (DST).