Banks County was created in 1858 from parts of Franklin and Habersham counties. It was named for Dr. Richard E. Banks, a circuit-riding physician who treated the settlers and Native Americans of northern Georgia and South Carolina.

The first county courthouse was completed in 1863. It was constructed of hand-made bricks in the Greek Revival style. It is on the National Register of Historical Places and now serves as a museum and office space.

Homer, the county's only municipality, was incorporated in 1859 and was named after Homer Jackson, a prominent settler. The northern boundary of Banks County is the Chattahoochee National Forest and much of the county is woodlands.