It was organized in 1870-1871 and renamed for General and Governor John Milton Thayer.

[2][3][4][5] In the Nebraska license plate system, Thayer County is represented by the prefix 32 (it had the thirty-second-largest number of vehicles registered in the state when the license plate system was established in 1922).

A local drainage, Big Sandy Creek, flows southeast and east through the northern part of the county, and another drainage, Rose Creek, flows northeastward through the SE corner of the county (they converge east of Thayer County's east boundary line).

[7] As of the 2000 United States Census,[16] there were 6,055 people, 2,541 households, and 1,689 families in the county.

31.50% of all households were made up of individuals, and 18.20% had someone living alone who was 65 years of age or older.

In only one national election since 1936 has the county selected the Democratic Party candidate (as of 2024).