Lake City is located at 45°43'30" North, 97°24'51" West (45.725000, -97.414167).
According to the United States Census Bureau, the town has a total area of 0.22 mi2 (0.58 km2). 0.22 mi2 (0.56 km2) of it is land and 0.01 mi2 (0.02 km2) of it is covered by water. The total area is 3.13% water.
Lake City is located in the Central Standard Time (CST) timezone, GMT-06:00. It observes Daylight Saving Time (DST).