The Atlanta Freethought Society (AFS) was founded in 1985 as a local, autonomous freethought group. Shortly after its foundation it affiliated as a local chapter of the Freedom From Religion Foundation (FFRF), a national freethought group; in December 1993 AFS voted to disaffiliate from FFRF after disagreements between the leaderships of AFS and FFRF.

Beginning in 1988 AFS entered into a six-year-long cooperative relationship with the Humanists of Georgia (HGA), a chapter of the American Humanist Association with roots dating back to the 1970's. The two groups held joint meetings and had a common presidency under the leadership of Tom Malone; from April to December 1994 they published a joint newsletter. Although a majority of AFS members voted to maintain some official relationship with HGA, HGA members voted in December 1994 to formally separate the two groups. At that time AFS adopted its current bylaws (since amended on several occasions) and elected Ed Buckner as President. AFS was also incorporated as a 501(c)(3) non-profit, member-run, educational organization.

AFS remains committed to friendly and cooperative relations with other freethought, humanist, and atheist groups (including the Humanists of Georgia; the Alabama Freethought Association, an FFRF chapter; the Birmingham Freethought Society, a member of the Campus Freethought Alliance; and many others). Since 1996 AFS has participated in the Alliance of Secular Humanist Societies, a national network sponsored by the Council for Secular Humanism for mutual support and cooperation among local and regional secular humanist, atheist, rationalist, and freethought organizations.

Beginning in the spring of 1995 the late Sam Howell donated over $13,000 to the society in gifts and a bequest in his will for the eventual acquisition of a permanent AFS homeplace. In recognition of his generosity the society voted to name the current AFS library the "Sam Howell Library", and to give that name as well to any future library located in an AFS homeplace. The society has also voted to name a conference room in our future homeplace after AFS member Dorothy Anne (Dot) Larson, a founding member of both the Atlanta Freethought Society and the Humanists of Georgia and a longtime freethought activist and leader.

Kimberly Lyle-Wilson was elected President of the society in 1996 and re-elected in 1997 and 1998. Gordon Shippey served as President Pro Tem after her resignation in June 1998; Judy Thompson was elected in a special election in July to complete the 1998 term. Our current President is Steve Yothment.

AFS has published several books, including an annual freethought calendar, complete with freethought quotations and classic freethought cartoons; Quotations That Support the Separation of State and Church, edited by Edward M. Buckner and Michael E. Buckner, a compendium of original quotations from the American Founding Fathers and others in support of religious liberty and church-state separation; and Bible Bloopers: Evidence That Demands a Verdict Too!, a reply by AFS member Michael Ledo to the works of Josh McDowell and other Christian apologists.