Harrisburg is a village in western Boone County, Missouri, United States. It is part of the Columbia, Missouri Metropolitan Statistical Area. The population was 266 at the 2010 census. It was founded to be an important railroad depot, but the railroad never came and the town remained small. Harrisburg is situated on a high point between Moniteau Creek and P…Harrisburg is a village in western Boone County, Missouri, United States. It is part of the Columbia, Missouri Metropolitan Statistical Area. The population was 266 at the 2010 census. It was founded to be an important railroad depot, but the railroad never came and the town remained small. Harrisburg is situated on a high point between Moniteau Creek and Perche Creek, at the headwaters of Callahan Creek. It is named in honor of John Woods Harris, an early county leader and owner of the nearby “Model Farm” on Thrall’s Prairie.