Opened in 1967, the park takes its name from the six flags that have flown over some part of Georgia during its long history—Spain, France, Great Britain, the United States, the Confederacy, and the state of Georgia.

The name Six Flags Over Georgia is a historical reference to the six different national flags that have flown over the land that is now the state of Georgia throughout its history. This naming convention started with the original park, Six Flags Over Texas, and was carried over to the Georgia location when it opened in 1967 as the second park in the chain. The six flags represented are: Spain, France, Great Britain, the United States of America, the Confederate States of America, and the State of Georgia. Historically, the park was divided into themed sections corresponding to these different eras, though in 2026, many of these areas have been renamed or reimagined to focus more on modern entertainment brands like DC Comics and Looney Tunes (e.g., the former "Confederate" section was renamed "Peachtree Square" in 2008). The name serves as a tribute to the diverse cultural and political heritage of the American South, originally envisioned by founder Angus G. Wynne as a way to combine regional history with world-class amusement park thrills, creating a "patriotic" and educational atmosphere for families.