Carl Kennedy, the girl's alleged abductor and biological father, was arrested.
Authorities said the arrest stemmed from an anonymous tip.
Just before Kennedy was arrested, officers learned he had painted his car black in order to avoid detection. The AMBER Alert notification listed the vehicle as a gold Suzuki.
The Randolph County Sheriff's Office said that, despite the color change, the car was still recognized by a concerned citizen.
Police said that Emma Kennedy appears to be in good health and is being evaluated at a local hospital.
"My main goal was to get her out of the house and get her safety in case something else was in there we didn't know about, a threat of any kind," said deputy Jimmy Barnes, who got Emma out of the house. "Just making sure she was safe that was the main thing."
Stay on top of breaking news stories with the ABC11 News App
An AMBER Alert was issued for Emma Monday morning after police said Carl assaulted her mother at a Virginia gas station.
The man, a registered sex offender in North Carolina, then took the child and fled. Police said he was believed to be armed with a knife.
Kennedy's sister Sylvia Kennedy told WGHP that she did not believe her brother would hurt his daughter and that there is a good reason why he did what he did.
"I'm just thankful that he is alive and Emma Grace is safe! There is (sic) two sides to every story, and I feel that he had a reason for taking his daughter like this."
Carl's last known residence is 2688 Valewood Drive in Asheboro.
He was convicted in 2014 of sexual battery, according to the NC Sex Offender Registry.