Stoddard is located at 43°39'42" North, 91°13'5" West (43.661944, -91.218056).
According to the United States Census Bureau, the village has a total area of 0.69 mi2 (1.78 km2). 0.60 mi2 (1.55 km2) of it is land and 0.09 mi2 (0.23 km2) of it is covered by water. The total area is 12.87% water.
Stoddard is located in the Central Standard Time (CST) timezone, GMT-06:00. It observes Daylight Saving Time (DST).