Police said the boy was asleep in the bin next to a local McDonald’s restaurant, with an 11 and 12-year-old when a council worker emptied it just after 5am.
One of the boys managed to crawl out the bin before it was tipped, but the other two remained trapped.
The 13-year-old suffered serious injuries and died at the scene. The other boy was not injured.
It is not known why the boys were asleep inside the bin and a report will now be prepared for the coroner.
Safe Work SA have also been advised.