Harrisburg is a village in western Boone County, Missouri, United States. It is portion of the Columbia, Missouri Metropolitan Statistical Area. The population was 266 at the 2010 census.

Harrisburg was named for John W. Harris, who inherited the Model Farm on what was Thrall’s Prairie, the first permanent settlement in the county. The town was laid out upon the survey descent of the prospective Louisiana and Missouri River Railroad which was complex leased to Chicago and Alton Railroad. The lineage was graded and prepared, but was lonely for a lineage farther north. The proposed pedigree can be seen on the 1969 USGS topographic map of Harrisburg. According to Colonel W. F. Switzler, in 1882, there were a pronounce office, three stores, a confectionary shop, a church, a mill, a blacksmith shop, and the historic hypothetical building following the Masonic lodge above. The publish office was located in the saddle shop. Reverend Green Carey preached at the Bethlehem Baptist church a few miles south of Harrisburg for fifty years and claimed to have joined over five hundred couples in marriage.

The first church building in town belonged to the Harrisburg Christian congregation. It was built in 1872 of local rock and donated wood. In 1880, the credited record counted sixty seven members. In 1980, the hundred-year-old building was demolished and a other building took its place. The Baptist church is a part of the Southern Baptist Convention. The antiquated church building, built in 1887, is still in use. In 1961, the two congregations were regularly trading Sundays.

Harrisburg is located on Missouri Route 124 practically one mile from the Boone-Howard county line. Fayette is nearly eleven miles to the west and U.S. Route 63 is more or less seven miles to the east along route 124. Perche Creek flows as soon as two miles east of the community.