After the success of his original Six Flags Over Texas park in Arlington, Texas, park founder Angus Wynne began searching for a location for a second park, looking mainly in the Southeastern United States, with initial design work on the park starting in 1964. In August 1965, the Wall Street Journal reported that Wynne's development company, Great Southwest Corporation, had purchased 3,000 acres (1,200 ha) of land along the Chattahoochee River outside of Atlanta for a planned $400 million industrial park with an adjacent $7 million amusement park. The land chosen was the site of the oldest permanent agricultural village in Georgia, home to Muscogee farmers from 200 BC to 500 AD. During development of the park the mounds were destroyed without being studied. The park itself sits on former dairy farm land known as Cole Brothers Dairy. The Cole Brothers sold their farm to Six Flags in the mid-1960s

Wynne hired former Hollywood art directors Randall Duell and Hans Peters to develop the park, then named "Georgia Flags". Like its sister park in Texas, the design and theming of Six Flags Over Georgia was inspired by six different flags that have flown over the state (or, perhaps more accurately, the lands that are now part of it) during its history. The two states shared the connections to Spain, France, Confederate States of America, and the U.S.; for Georgia, Great Britain would replace Mexico, and the flag of the state of Georgia would replace that of Texas, even though Georgia was never a sovereign nation, as Texas once was. When Six Flags Over Georgia opened in 1967, Six Flags became the first theme park operator in the United States to operate parks at multiple locations.

Six Flags Over Georgia opened to the public on June 16, 1967. Attractions first available included the Log Jamboree log flume ride, Jean Ribaut's Adventure (a boat tour similar to Disney's Jungle Cruise attractions), the Six Flags Railroad, two driving attractions (the Happy Motoring Freeway and the Hanson Cars), two Satellite flat rides, the Tales of the Okefenokee dark ride, the Casa Loco tilt house, the Sky Lift/Astro Lift cable car and the park's first roller coaster, the Dahlonega Mine Train. The park's live entertainment offerings included a dolphin show, the Krofft Puppet Theater and the Athenaeum, later renamed the Crystal Pistol.

After a successful first season, plans were set in motion to expand the park, and adjustments were made to existing attractions based on visitor feedback. A second Log Jamboree flume was added, a new show debuted in the Krofft Puppet Theater and the effects inside the Tales of the Okefenokee were upgraded with the help of Krofft Studios. The park relocated Casa Loco out of its Spanish fort to make way for the Horror Cave haunted house attraction; a new adjacent building was built for Casa Loco's effects, which would become Casa Magnetica. However, the largest improvement was the addition of the park's first new section, Lickskillet. Located outside the park's railroad tracks and named after a Georgia mining town in the late 19th century, Lickskillet added three new rides — the Spindle Top (a Rotor flat ride, the Wheel Burrow (a Chance Tumbler) and the Sky Buckets, the park's second cable car ride — along with several craft shops and a shootout show performed on the street. In 1969, Six Flags added still more attractions, the Sky Hook observation tower, which was relocated from Six Flags Over Texas, the Mini Mine Train, the park's second roller coaster and the Chevy Show domed theater building.

In the early 1970s, Six Flags began augmenting its supply of costumed characters with creations from various Sid & Marty Krofft television series. Characters from H. R. Pufnstuf began appearing in the park in 1970, with characters from Lidsville added in 1972. The 1970 production in the Krofft Puppet Theater was based on H. R. Pufnstuf, as well. These characters left the park after the 1974 season as Krofft decided to open its own amusement park, The World of Sid and Marty Krofft, in downtown Atlanta. In Lickskillet, the Drunken Barrels flat ride had replaced the Wheel Burrow, and in 1972 Six Flags debuted the fully-restored Riverview Carousel on a hilltop adjacent to the section. This carousel, purchased from the defunct Riverview Park in Chicago, was built into a pavilion modeled after its original home.

For the 1973 season, Six Flags added its second park expansion, the Cotton States Exposition, a development four years in the making. In 1969, general manager Errol McKoy first proposed that the park install a wooden roller coaster, an idea to which Angus Wynne wasn't very receptive. By 1971, however, the concept was approved, and designer John C. Allen and the Philadelphia Toboggan Company were contracted to design the ride, which opened in 1973 as The Great American Scream Machine. The Scream Machine, the largest roller coaster in the world at the time, was the anchor attraction for the Cotton States area, which was inspired by the 1895 Cotton States and International Exposition. In 1974, Six Flags added two new rides, the Mo-Mo the Monster Octopus ride in the USA section and the Phlying Phlurpus spinning ride in Cotton States; Mo-Mo would later move to Cotton States, as well. The Spanish section received a number of children's rides for the 1975 season. After the end of that season, the Happy Motoring Freeway was removed to make way for the Great Gasp parachute drop, which would be the park's new attraction for 1976.

In late 2010, Six Flags began the process of removing licensed themeing from attractions. They terminated several licenses including their license with Thomas the Tank Engine. Thomas Town was renamed and rethemed to Whistlestop Park in time for the 2011 season. In an arrangement similar to that for Six Flags Over Texas, it is owned by a group of approximately 120 limited partners—some the heirs of Angus G. Wynne—and is managed by the corporation. In years past, this has caused significant friction, including legal action. Starting in 1991, the park was managed by Time Warner Entertainment. The partners sued Time Warner in 1997, claiming that they had neglected to invest in the park and overcharged the partners for the improvements it did receive. A Gwinnett County civil court jury agreed and awarded the partners damages in excess of US$600 million. In 1998, Time Warner sold its interests in the Six Flags parks to Premier Parks of Oklahoma City, which later changed its name to Six Flags Theme Parks, Inc.

On August 29, 2013, Six Flags officially announced it would add a Hurricane Harbor water park next door to the park for the 2014 season. In late April 2014, the park announced that it will expand their season from October to January, to include the new Christmas event, Holiday in the Park for years to come.

As part of Six Flags' 2015 capital investment program, Six Flags Over Georgia received two rides in its Gotham City section. The first, "The Joker: Chaos Coaster" is a Larson Giant Loop ride approximately 70 feet in height, while the second, "Harley Quinn Spinsanity", is a more traditional Tilt-A-Whirl family ride. Both attractions were part of a broader renovation of Gotham City, which also included a new character meet-and-greet area and improvements to the existing Gotham City Eatery restaurant.

In 2016, Six Flags added two new children areas to the park – Bugs Bunny Boomtown and DC Super Friends, the first in the Six Flags chain. On June 16, 2016, it was announced that Dodge City Bumper Cars would be closed and removed from the park to make room for a new ride in 2017. On September 1, 2016, the park announced that an all new dark ride named Justice League: Battle For Metropolis would replace Dodge City Bumper Cars.

In December 2024, Six Flags announced that they would take full ownership on the park and White Water from its partners for $332 million, of which the transition will occur at the beginning of January 2027.