Shawn Martinez had been last seen leaving his home at 270 Wortman Avenue in the East New York section.
Police say the boy is in good physical and mental condition.
He is a foster child, and it is believed that he ran away from his foster home in Brooklyn to be with his biological mother.
Police Commissioner Ray Kelly says the boy was found in Fayetteville, North Carolina, on a bus headed from Florida to New York.
Kelly said it appears Shawn had gone to visit his mother in Florida.
He is currently with a child services agency in North Carolina.
The Missing Child Alert issued by the New York State Missing Person Clearinghouse.on behalf of the NYPD was cancelled Wednesday morning.