Harrison County was formed on December 21, 1793 from portions of Bourbon and Scott Counties. Harrison was the 17th Kentucky county in order of formation. It was named after Colonel Benjamin Harrison, an early settler in the area. Cynthiana was named after Robert Harrison's two daughters, Cynthia and Anna.
The center section of the court house was built in 1851 in the Greek Revival Style. The north and south "wings" were added in the early 1900s.