The boy was found critically injured outside a medical centre in Craigieburn, in Melbourne's north, about 7.50pm on Wednesday.
A staff member from the medical centre rushed to his aid and delivered CPR, but was unable to prevent the boy from dying at the scene.
In a previous statement released on Wednesday night, police said a crime scene had been established and the boy, from Mickleham, had yet to be formally identified.
About 5.30am on Thursday, a 16-year-old boy and a 20-year-old man were arrested in the nearby suburb of Pascoe Vale.
They will be interviewed by homicide squad detectives, Victoria Police said.
Northern Health, which operates the medical centre, said it had no knowledge of the circumstances leading up to the young man being found.
"A staff member discovered a young man in the hospital car park with serious injuries," a spokesperson for the organisation said.
"Despite the immediate efforts of hospital staff and emergency responders to provide assistance, the young man sadly died from his injuries.
"Our thoughts are with the young man's family and loved ones during this difficult time."
The investigation is ongoing.
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