Police initially arrested and charged the boy with weapons offences in December after the NSW Joint Counter Terrorism Team received reports of someone making violent threats online, the Australian Federal Police said in a statement on Wednesday morning.
During a search of the boy's inner-west Sydney home, police allegedly found a flick knife and a gel blaster, charging him with possessing an unauthorised pistol and a prohibited weapon.
A number of electronic devices were also seized.
While the devices were being investigated, the teenager faced court and was eventually bailed on the weapons charges.
A review of the devices then allegedly uncovered violent extremist material and documents containing information that could help carry out a terror attack.
"It will be alleged the young person held a mixed ideology and outlined plans for acts of violence," the AFP said.
On Tuesday, the boy was charged with five terrorism offences, including collecting and making documents likely to facilitate a terrorist act.
The weapons charges carry a maximum sentence of 14 years in jail, while the most serious of the terrorism charges have a maximum sentence of 15 years behind bars.
The teenager is expected to appear at a children's court on Wednesday.
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