Audubon county was named after the famous naturalist, John James Audubon, who died in 1855.
During the first year of organization, court was held in a schoolhouse in Hamlin's Grove. However, in 1861 the county seat moved to Exira, which began a long term battle between the two cities over which would be the county seat. In 1871, the board of supervisors appropriated $6,948 to be used for building a new courthouse in Exira. But the project was held up when the county seat fight re-developed. The citizens of Hamlin wanted the honor of being the county seat again. In the end, Exira was successful in its bid for the courthouse and the building was erected for about $2,200.
The county seat moved again in 1879 to Audubon and in 1884 the county secured a $7,000 building to be used as the courthouse. Upon completion, the building was a two-story brick building with stone trim, measuring 44 by 100 feet, with a central tower. This courthouse was demolished in 1939.
That same year, a ninety-six year old Civil War veteran turned the first shovelful of dirt to commence the construction of the present courthouse. On June 11, 1940, the county celebrated the dedication of the new brick courthouse with stone trim. It was built for about $130,000.