A tearful Cox said Monday that she will resign as the state's school's chief June 30.
Gov. Sonny Perdue said he will appoint a new superintendent to take over the remainder of her term.
Cox, a Republican, had been planning to seek a third term and was facing stiff opposition.
But she said that after qualifying to run for re-election she was offered a job as chief executive officer of the U.S. Education Delivery Institute, a new Washington D.C-based group designed to help states implement strategies to boost student achievement.
Cox was in her second term as Georgia's schools superintendent. She had also served two terms in the Georgia House of Representatives.