Clarke Co. GAClarke County was created in 1801 by an act of the Georgia General Assembly on December 5. The county was named after Revolutionary War hero Elijah Clarke and included 250 square miles (647.5 km2) of land that was originally part of Jackson County. Clarke was most recognized for being credited with the 1779 victory at the Battle of Kettle Creek in Wilkes County. The Elijah Clarke Chapter of the Daughters of the American Revolution erected a monument in his name in the middle of Broad Street in Athens that still stands today.

Two skirmishes took place in Clarke County during the American Civil War in 1864, one near Barber's Creek and the other off of Mitchell's Road. An occupation garrison arrived in Athens on May 29 and a provost-marshal government was set up temporarily. Formal military occupation of the area ended before the end of 1864, although federal occupation continued until early 1866.

The original Clarke County Commission had selected Watkinsville, now in Oconee County, as the county seat. All county offices and county business, including the courts and jail, later moved north to Athens when the seat was moved on November 24 of 1871. For four years, county meetings were held in the old town hall in Athens until 1876 when a new courthouse was constructed in the area bounded by Prince Avenue, Hill Street and Pope Street. The current courthouse in use today was later erected on the corner of Washington and Jackson Streets downtown in 1914.

On February 12, 1875, to placate county residents still angry over the relocation of the county seat to Athens three years earlier, the state legislature created Oconee County from the southwest section of Clarke County and named Watkinsville as its seat. Oconee gained one-third of Clarke's population and three-fifths of its land.

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