Before its organization Clay County was attached to Woodbury County for judicial and civil reasons. After its independence was declared, an election was held on October 12, 1858.

It was held at the home of A. S. Mead and its purpose was the election of county officials. Of the 18 men who voted, 14 were elected to an office. Those offices were kept in the homes of the officers until 1859. At this time A. W. Hubbard, Judge of the Fourth Judicial District, authorized a commission to locate a county seat. 

On July 16, 1859 the commission chose the present site of Spencer. But, due to the fact that Spencer was unimproved and no settler lived within a 10-mile radius, it was refused by the residents of Clay. In May 1860 the county judge received a petition asking that the county seat be located at Peterson. An election was held, and all 10 participants voted in favor

of Peterson. Soon afterwards a courthouse was built at a cost of $6,000.

The county seat remained in Peterson until 1871. In 1871 the town of Spencer was formally laid out, and since it was more centrally located than Peterson, the question of moving the county seat was asked again. It was answered in an election held in October of that same year; Spencer won the county seat by a margin of 159 votes. 

The first courthouse was built by the residents of Spencer.

They formed a stock company and sold shares. Those who could not afford a share offered their labor. When the building was completed, it was sold to the city for $1,333.  A second building was built in 1884 at different location. It was criticized by the residents as being plain and boring. It was the best that the county could do because they were held to $5,000 by the law. It was decided in 1900 that the county needed a new courthouse. The structure was erected on the same site as the second and was ready for occupation in September 1901.

No formal dedication was held: the doors were just opened and business continued. This building is no comparison to the second. Costing $60,000, $3,000 on marble alone, it is a beautiful structure.The population of Clay County increased approximately 30% since the 1901 Courthouse was completed. So in 1979, the Board of Supervisors decided to renovate the existing courthouse and construct an administration building. 

The motion passed in August and $2.1 million was approved for the two projects. A dedication ceremony was held on September 26, 1982, and Clay County now has Two building of which to be proud. Source: History Of Clay County, 1986.