Seven people were inside the residence at the time with one man sustaining minor injuries and transported to hospital.
Western Australian detectives charged the teenager after the drive-by shooting took place at Gosnells, a Perth suburb, around 12.30am on Saturday.
The boy allegedly fled the scene and was later arrested at a car-park on late Sunday.
But police say the rifle he used has not been found.
The teenager was charged with eight offences including unlawful use of a firearm, endangering life and no authority to drive.
Acting Senior Sergeant Heath Atkinson said the incident was disturbing
"This is a shocking and deeply concerning incident that a 13-year-old child is alleged to have access to a firearm and to have discharged it at an occupied home," he told reporters on Monday.
"The consequences could have been far worse.
"When a child gains access to a firearm it creates an unacceptable risk to that child and to the wider community."
The bullet-riddled home sustained damage to the external brickwork, roof guttering and a glass window.Â
The 13-year-old appeared briefly in Perth Children's Court on Monday and did not apply for bail.
He is reportedly out on bail on charges from his home state of Victoria.
Police believe this to be an isolated incident with no ongoing risk to the community.
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