With its location near the Missouri River, an important early transportation link, Pawnee was among the first counties in the state, having been organized in 1856. After two elections in 1856, Pawnee City, which at the time was an area identified only by its township and range legal description, was selected as the county seat. The first courthouse was not built until 1869. By the turn of the century, county residents were prepared to replace the aging and poorly constructed stone building with a more substantial structure. In 1910 voters approved a bond issue to finance a new courthouse.

The Classical Revival-style building, listed on the National Register of Historic Places, was completed in 1911, and is one of ten courthouses designed by W.F. Gernandt. It was renovated in 1999, landscaped, and made handicap assessable.