Winnebago is a village in Thurston County, Nebraska, United States. The population was 768 at the 2000 census.
Winnebago is located at 42°14′14″N 96°28′18″W / 42.23722°N 96.47167°W / 42.23722; -96.47167 (42.237167, -96.471582). It is located within the Winnebago Reservation of the Ho-Chunk.
According to the United States Census Bureau, the village has a total area of 0.3 square miles (0.7 km²), all of it land.