On April 2, 1937, Nicanor Gordo and Joaquim Veiga founded the club, starting football in the newly founded city of Goiânia. Nicanor Gordo and Joaquim Veiga left the newly founded club in 1938, and joined Goiânia Esporte Clube, which was another new club.

In 1944, the club competed in the first Campeonato Goiano, which was also the first official football championship in the state, and was contested between five clubs from Goiânia. The other teams were Goiânia, Vila Nova, Goiás and Campinas. Atlético Goianiense won the competition, being its first title. In 1957, the club won the state championship without losing a match, also winning the Torneio dos Invictos, played in the same year.

In 1971, the team won the Torneio da Integração Nacional, beating Ponte Preta in the final. In 1990, after defeating América Mineiro in the penalty shootout, Atlético Goianiense won the Campeonato Brasileiro Série C.

In 2003, Atlético Goianiense finished in the state championship's last place, and was relegated to the following year's second division. In 2005, the club won the Goiás State Championship Second Division, being promoted to the following year's First Division. In 2006, the club finished in second place in the Goiás State Championship First Level, and they won the league in 2010 and in 2011.