The boy was pulled over in Broken Hill in the New South Wales (NSW) outback after a patrol noticed the car's bumper dragging on the ground.
Police said the boy had been attempting to drive 4,000 km from Kendall in New South Wales to Perth, Western Australia.
Local media reported that the boy managed to evade suspicion partly because he looks much older.
The manager of a petrol station in the town of Cobar was quoted as saying that he looked "maybe 19 or 20".
More From This Section
"He'd taken the family car," Detective Inspector Kim Fehon was quoted as saying by the Australian Associated Press news agency.
"His parents reported him missing immediately after he left home, so they were looking for him," he said.
The boy had seemingly driven across the entire state of New South Wales, after setting off from Kendall near Port Macquarie on the east coast.
A NSW Police spokesperson said the boy was stopped by Highway Patrol officers at about 11 AM Saturday when they noticed his car's bumper was dragging along the ground.
"Checks revealed the driver to be a 12-year-old boy travelling from Kendall NSW on his way to Perth," the spokesperson said.
The boy was arrested and taken to Broken Hill police station.