The child's parents reported him missing Thursday, but police didn't find him until Saturday at the airport in Malaga, Spain, Euronews.com reported Sunday.
The child managed to pass through airport security at the Brussels facility without a boarding pass or identification, officials said.
Airport and Jet Air airline officials said they were reviewing security video to see how the child managed to board the flight.
Euronews.com said the reason why the boy took the flight was unclear. His mother said he ran away after a dispute with a teacher.