Naponee (Mississauga: naapanne;[4] "flour") is a village in Franklin County, Nebraska, United States.

According to the United States Census Bureau, the village has a total area of 0.23 square miles (0.60 km2), all land.

There were 12.2% of families and 12.3% of the population living below the poverty line, including 12.5% of under eighteens and 6.5% of those over 64.

Naponee's name originates with Napanee, Ontario, the hometown of a Canadian who fought in the Civil War and bought land along the Republican River.

Like many places, Naponee suffered in the Great Depression and major dust storms and flooding of the Republican River in 1935 compounded these woes.

Construction of the nearby Harlan County Dam in the 1940s nearly doubled the population from 200 to 400.

Today Naponee remains a rural community with a stable population.