Milligan is a village in Fillmore County, Nebraska, United States.

[3] Milligan was laid out in 1887 when the Kansas City and Omaha Railroad was extended to that point.

[5][6] According to the United States Census Bureau, the village has a total area of 0.24 square miles (0.62 km2), all land.

There were 170 housing units at an average density of 708.3 per square mile (273.5/km2).

The racial makup of the village was 98.10% White, 0.95% Native American, and 0.95% from two or more races.

Milligan and the neighboring village of Exeter make up part of the Exeter-Milligan School District.

It serves as a meeting hall in the Czech community, and was added to the National Register of Historic Places in 1996.