The first Wabasha County commissioners leased a hall to serve as a courthouse because they believed that the citizens had not had an opportunity to vote on the location of the county seat, and there were were so few settlers (less than 400) that the "cost to the individual to build a courthouse would be burdensome." The first court term was held in a warehouse in 1856. After hearing a few motions and granting a few naturalization papers, court adjourned.
Lake City forced a county seat election in 1860 and received a majority of the votes. However, oddities in the results led to the proposal's defeat. In the meantime, a 40 by 45 foot, two-story stone schoolhouse had been built in Wabasha. In an effort to keep the county seat there, the city donated the school to the county for use as a courthouse. Wabasha survived further county seat battles over the years.
The original part of the current courthouse cost $25,700 to build in 1892. Its Romanesque Revival style is not apparent today. The tower that once rose from a corner pavilion was its most prominant feature. It had a lookout with arched openings at the fourth floor and a tall peaked roof with a finial. The tower was removed in 1939 and the roof squared off and flattened.
A large addition of matching red brick was added in 1970 and forms an "L" on the west end extending toward the north. Eckert and Carlson from Winona designed the $174,495 addition. The inside has also been carpeted and combination windows have been installed. However, the original wooden wainscoting still remains.