The 12-year-old boy was not wearing a helmet or protective clothing when he was thrown from the bike and struck a gutter on Saturday, police said.
The boy was taken from the scene at Hastings, south of Melbourne, to the Frankston Hospital, then was flown to the Royal Children’s Hospital.
Police gave the boy first aid before paramedics arrived.
The mini bike was not registered.
Police are investigating the circumstances that led to the crash.