In 1871, residents in Clay County in northwestern Iowa voted to move the county seat from Peterson to Spencer. The first two courthouses were built at a combined cost of $6,500 and were criticized by citizens as being “plain and boring” in comparison to other equivalent facilities across the state. In 1900, construction was started on a new $60,000 Clay County Courthouse, and the doors were opened to the public on September 1901.

In 1979, the Clay County Board of Supervisors dedicated $2.1 million to renovate the courthouse and construct a separate administration building. The projects were completed in 1982. The Clay County Courthouse is one of eight buildings in the county on the National Register of Historic Places. It was added to the list in 1981.