A special agent in Charlotte learned of information that led them to find Burns, now 17, at a home in Duluth, Georgia.
Michael Ren Wysolovski, 31, was taken into custody and is facing a number of state charges, the Federal Bureau of Investigation said.
FBI Charlotte and the Charlotte-Mecklenburg Police Department will continue their investigation into Burns' disappearance and will be working closely with FBI Atlanta and the Gwinnett County Police Department.
Before her disappearance, Burns had last been seen at her home on Baldwin Drive at 12:30 a.m. on May 23, 2016.
Her parents told WSOC that when they woke up that morning they found their door was unlocked and their daughter was gone.
She was recovered at a home in the 2700 block of Seneca Trail.
Wysoloyski faces a number of charges, including false imprisonment, aggravated sodomy, interference with custody and cruelty to children involving first-degree deprivation.
Neighbor Jennifer Elmore says Wysoloyski moved into the home just months ago and kept to himself.
"The blinds would always be closed, night and day. I did see a younger female with him but I didn't think anything of it at all," said Elmore.
According to North Carolina station WBTV, Burns' father said she left a diary behind in May of 2016 that detailed a plan to run away with a 32-year-old man she met online. Family members said Burns has Asperger Syndrome.
Wysoloyski is scheduled to hear a formal reading of his charges Monday afternoon in a small courtroom inside the jail.
CNN contributed to this report.