Authorities found Leiby Kletzky's dismembered body inside the home of a man who had seen the boy around the time he vanished.
Kletzky approached the suspect, Levi Aron, 35, when he got lost, according to surveillance video. When police tracked down Aron, he made statements implicating himself in the boy's death.
He nodded towards the kitchen when authorities asked him where the boy was. Detectives saw blood on the freezer door. When they opened it, they found bloody knives, a cutting board and feet, an official told the Associated Press.
More body parts were located inside a suitcase that was in a trash bin in another Brooklyn neighborhood.
The medical examiner's office will determine a cause of death and positive identification.
Police said it does not appear that Aron had previous contact with Kletzky or his family, according to WABC-TV in New York.
Aron panicked when he saw the coverage of the search and killed the boy, authorities said.
The break in the case came when investigators focused on a grainy surveillance video that showed the boy, wearing his backpack, walking down the street, while a man walked nearby.
Detectives noticed the man on the video going into a nearby dentist's office, Browne said. The dentist, located later in New Jersey, said he remembered someone coming by to pay a bill for a patient, and police were able to identify Aron using records from the office.
The Associated Press contributed to this report.