The Darwin boy appeared in the Children's Court on Thursday following a joint investigation by Australian Federal Police, Northern Territory Police and the Australian Security Intelligence Organisation.
The NT Joint Counter Terrorism Team began an investigation earlier in October after receiving information via Crime Stoppers about violent extremist material posted online by an Australian user.
Police searched the boy's home on Wednesday and allegedly found violent extremist material and instructions for making 3D-printed guns.
Inquiries revealed the teen operated social media channels where it's alleged he accessed, discussed and reposted extremist material.
AFP Detective Acting Superintendent Pixie Fuhrmeister told reporters in Darwin on Thursday there was no information the boy had access to firearms or had the capability to make one.
"The seized material indicates a mixed ideological motivation, with the glorification or support for a mass casualty attack at a school or place of worship," she said.
Police across Australia were becoming more concerned about the number of young people becoming radicalised online, Supt Fuhrmeister said.
"We are facing one of our greatest challenges in history, with the radicalisation and manipulation of our youth."
NT Police Commissioner Martin Dole said there was no ongoing threat to the community following the boy's arrest but it was important not be complacent about the threat of terrorism.
"There is no place for violent extremism in the Northern Territory."
Parents should be aware of what their children were looking up and should be looking for behavioural changes, and if they see changes, get help, Mr Dole said.
"If you think there's a risk, report it."
The teen was charged with collecting or making documents likely to facilitate terrorist acts, carrying a maximum penalty of 10 years in prison.
He was further charged with possessing violent extremist material obtained using a carriage service, carrying a maximum penalty of five years' imprisonment.
A third charge against the teen was that of possessing or controlling firearms and explosives manufacture material obtained or accessed using a carriage service, carrying a maximum five years in prison.
AFP Counter Terrorism Commander Paula Hudson said on Thursday the speed and scale of radicalisation was becoming significant challenge, especially when it came to young people.
''It is well-documented that terrorists and violent extremists use the online environment to radicalise vulnerable individuals, and technology is enabling this to occur a rapidly increasing rate," she said in a statement.
A whole-of-society effort was needed to protect young people from radicalisation and manipulation, Commander Hudson said.
''Without a serious intervention, the risk is our justice systems, mental health systems, education systems and financial systems will become overwhelmed by youth victims and perpetrators."
The accused teen has been remanded to appear in court again on November 9.
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