An Amber Alert had been issued for Hunter Allen Thompson early Tuesday morning; he had been reported missing Monday night.
Hunter was taken to a hospital for an examination, which is routine, Anderson County Sheriff's Capt. John Skipper said. "And he is fine," Skipper said.
Hunter was left at a grocery store by someone in a car, officials said. Investigators said they were looking for a white man with brown hair, wearing a white pullover shirt and gray shorts. He was last seen driving toward Interstate 85 in a white, four-door car.
Skipper declined to give other details, including what the boy told officials.
The boy had vanished from the Kmart as he looked at video games while family members were shopping elsewhere in the store, authorities said earlier Tuesday.
At the Kmart, emergency crews cheered when search coordinator Dale Horn told them the boy had been found.
"We did a good job, we found him," Horn told the rescue teams.
It was the third time the Amber Alert system had been activated in South Carolina, the State Law Enforcement Division said.
An Amber Alert for a missing child goes to media outlets and lottery retailers and activates highway traffic advisory signs. The program is named for Amber Hagerman, a 9-year-old Texas girl who was abducted and killed in 1996.