The new county was named in honor of Revolutionary War Lieutenant Colonel, Congressman, Senator and Governor James Jackson.

In 1801, the Georgia General Assembly granted 40,000 acres (160 km2) of land in Jackson County for a state college.

Franklin College (now University of Georgia) began classes the same year, and the city of Athens was developed around the school.

Also the same year, a new county was developed around the new college town, and Jackson lost territory to the new Clarke.

The county seat was moved to an old Indian village called Thomocoggan, a location with ample water supply from Curry Creek and four large springs.