Police said the boy is being medically evaluated.
There had been an intense search for Charlie Bothuell V since his reported disappearance June 14, and police just hours earlier had told reporters that they weren't ruling out the possibility of homicide.
"There are a lot of questions that need answering," Detroit police Chief James Craig told ABC News.
In an earlier search of the premises, "the dogs didn't react, and we went through the entire home," Craig said.
Officers discovered the boy while serving a search warrant on the home that he shares with his father and stepmother. Charlie was hiding in the basement behind boxes and a large plastic drum.
There was food nearby, the Detroit News reported on its website.
Charlie's father, Charlie Bothuell IV, said he was shocked that his son had been found.
"For anybody to imply that I somehow knew that my son was in the basement, it's absurd and it's wrong," the Detroit News quoted Bothuell as saying.
"I love my son. I'm glad that he's home, and he's going to have the great future that he deserves to have."
Police said it wasn't clear if the boy had been in the house the entire time. When found, he was described as hungry but appearing to be fine.
Police say the father took a polygraph test while his son was still missing, but the stepmother would not.