Fontenelle is located at 41°59'5" North, 110°3'29" West (41.985000, -110.058333).
According to the United States Census Bureau, the city has a total area of 3.59 mi2 (9.31 km2). 3.45 mi2 (8.94 km2) of it is land and 0.14 mi2 (0.36 km2) of it is covered by water. The total area is 3.91% water.
Fontenelle is located in the Mountain Standard Time (MST) timezone, GMT-07:00. It observes Daylight Saving Time (DST).