Autauga County was established on November 21, 1818 by an act of Alabama Territorial Legislature (one year before Alabama was admitted as a State). As established, the county included present-day Autauga County, as well as Elmore County and Chilton County. At the time, Autauga (aka, Tawasa) Indians lived here, primarily in a village named Atagi (meaning "pure water") situated on the banks of a creek by the same name (called "Pearl Water Creek" by settlers). Autaugas were members of the Alibamu tribe. They sent many warriors to resist Andrew Jackson's invasion in the Creek War. This county was part of the territory ceded by the Creeks in the Treaty of Fort Jackson in 1814. The first county seat was at Jackson's Mill, but the court only met there long enough to select a permanent seat at Washington, built on the former site of Atagi in the southeast corner of the county. In 1830 the county seat was moved to a more central location at Kingston and the town of Washington dwindled until it was completely deserted in the late 1830s.

Daniel Pratt arrived in Autauga County in 1833 and founded the new town of Prattville, north of Atagi on the fall line of Autauga Creek. His cotton gin factory quickly became the largest manufacturer of gins in the world and the first major industry in Alabama. It was at his factory, and with his financial backing, that the Prattville Dragoons, a fighting unit for the Confederacy was organized in anticipation of Civil War. Other units formed in Autauga County included the Autauga Rifles (Autaugaville), The John Steele Guards (western Autauga Co.) and the Varina Rifles (northern Autauga Co.). None of the fighting of the Civil War reached Autauga County and Pratt was able to secure payment of debts from Northern accounts soon after the war, lessening the disabling effects of the Reconstruction period in the county.

Charles Atwood, a former slave belonging to Daniel Pratt bought a house in the center of Prattville immediately after emancipation and was one of the founding investors in Pratt's South and North Railroad. The presence of such a prominent African-American family owning land in an Alabama city as early as the 1860s is exceptional.

In 1866 and 1868, Elmore and Chilton counties were split off from Autauga County, and the county seat was moved to the population center of Prattville, where a new courthouse was completed by local builder George L. Smith in 1870. In 1906, a new and larger courthouse was erected in a modified Richardsonian Romanesque style a block north of the older one. The building was designed by Bruce Architectural Co. of Birmingham and built by Dobson & Bynum of Montgomery.