Scott County was explored as early as 1774. One of the early settlers was John McClelland of Pennsylvania. The area became subject to hostile Indian attacks, and was abandoned by 1777.
In 1783, Robert Johnson established the first permanent settlement at Johnson's Station. In 1786, Maryland Catholics established the second parish in Kentucky at St. Francis, Kentucky.
Scott County was established in 1792 from land given by Woodford County. It was one of the first counties created after Statehood. It was named for Revolutionary War hero, Gen. Charles Scott, who led the Kentucky Militia at the disastrous Battle of the Wabash in 1791. Gen. Scott went on to the 1794 victory at the Battle of Fallen Timbers, and served as Governor from 1808 - 1812.
In 1825, the Choctaw Nation established the Choctaw Academy at Blue Spring in the county. They operated the school for Choctaw boys until 1842, when it closed. They transferred the staff and records to the Choctaw Nation, Indian Territory, where they had removed in the 1830s. There they founded the Spencer Academy in 1844 as the school for Choctaw boys and also founded a school for girls. Later in the nineteenth century, they accepted Baptist missionaries to found the Armstrong Academy.
On November 18, 1861, Scott County native George W. Johnson was elected provisional Confederate governor of Kentucky. In the American Civil War, Scott County furnished the Union army with 118 soldiers and the Confederacy with approximately 1,000.