Atheist Alliance International was founded in the United States as the Atheist Alliance in 1991 by four local US atheist organizations: Atheists United (Los Angeles, California), Atheist Coalition (San Diego, California), Atheists of San Francisco Region (California) and the Atheist Network (Houston, Texas). Atheist Alliance quickly added additional affiliates. Within a year, it had eight US organizations as members and by the end of 1992, its first international affiliate.
Atheist Alliance began publishing its magazine, Secular Nation, in the second half of 1994.
Atheist Alliance began hosting US conventions in 1995, with the first one held in Los Angeles, California. The Atheist Alliance website went online in 1997.
By 2001, the organization had a half-dozen affiliates outside the US, and so changed its name to Atheist Alliance International (AAI).
In 2006, AAI held its first international conference in Reykjavik, Iceland. In 2010, it began its current program of co-hosting conventions with Affiliate Members, starting with the extremely successful 2010 Global Atheist convention held in Melbourne, Victoria, Australia.
In 2010, AAI determined that it could more effectively pursue its goals by separating its US focused activities from its global activities. The US group, Atheist Alliance of America, became an Affiliate Member of AAI.
In 2017, the AAI Board decided to put more emphasis on directly supporting atheists around the world who are excluded, disparaged, discriminated against and criminalized.