After the end of the Civil War, during the era of Reconstruction, Kentucky worked to rebuild what had been destroyed by the acts of violence carried out during the war. Subsequently, the courthouse was rebuilt, with construction being completed on the new building in 1866. The courthouse stood in place of the previous building in Morehead for nearly fourteen years until the events leading up to the Rowan County War. The Rowan County War was fought between two warring factions from the Kentucky county, with the city of Morehead acting as the epicenter of the war. With its centrality to the events of the small-scale war, Morehead was the Rowan County city most afflicted by the acts of violence carried out during the fighting. A few years before the start of the war, the county courthouse, located in Morehead, once again became collateral damage, being burned again in 1880 during a small skirmish between the county's feuding factions.
After this, the courthouse was relocated to another building until it was eventually rebuilt again in 1899. As a result of each of the two burnings, all of the legal records housed in the courthouse prior to 1880 were destroyed, with no way to recover them.