Former state Sen. Kasim Reed edged out city councilwoman Mary Norwood by only 715 votes in the Dec. 1 contest. Under Georgia law, the runner-up can petition for a recount when the margin of victory is less than 1 percent of the total vote.
"We are looking forward to working out the process and making sure that all votes were counted accurately and we'll see what happens," said Norwood's campaign manager, Roman Levitt.
Elections chief Barry Garner said the recount is expected to take four to five hours.
The Fulton County Board of Elections certified the election result Saturday. More than 84,000 ballots were cast in the runoff - more votes than in the general election.
If Reed's win is confirmed, he will take Mayor Shirley Franklin's place Jan. 4.
"Mrs. Norwood has the legal right to request a recount, but her doing it today has really dragged out the process for healing the city and moving Atlanta forward," said Tharon Johnson, Reed's campaign manager.
Both campaigns will have representatives present during the recount.
Reed and Norwood waged a hard-fought battle across the city and over the airwaves in the month leading up to the runoff. Both tried to gain a critical mass of racial crossover votes, with victory likely hinging on black-versus-white turnout. Norwood was trying to become the city's first white mayor in more than three decades.