The boy died Sunday in the Tiwi Islands north of the city of Darwin, after running from the sea complaining that something had stung him, said Northern Territory Police spokeswoman Katie Fowden.
He was taken to a nearby medical clinic where staff were unable to resuscitate him, Fowden said.
"It would certainly appear to be a box jellyfish," she said, adding that an autopsy had yet to confirm the cause of death.
Northern Territory Health Department official Prof. Bart Currie said the tragedy was a reminder that people should not swim in Australia's tropical northern waters during the so-called "stinger season" from October through May.
Children are especially vulnerable to the jellyfish toxin, Currie said.
A 3-year-old girl and a 9-year-old girl died in similar circumstances on northern beaches last year.