18-year-old Tamim Khaja, of Macquarie Park in Sydney's northwest, who was arrested in Parramatta by Joint Counter Terrorism Team, is expected to appear at Sydney Central Local Court tomorrow.
Both offences carry a maximum sentence of life imprisonment.
He was arrested for plotting an "imminent" terror attack in Sydney and had tried to leave the country in February, police said.
"Since that time, he has been under the surveillance of the relevant authorities who have decided this morning to act to prevent an imminent terrorist event," Attorney-General George Brandis told reporters, without giving details of potential targets.
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Police alleged that the teen was scouting for possible sites in Sydney to launch an attack and had been trying to get a firearm.
He tried to board an international flight from Sydney Airport in February, they said. However, he was stopped because his passport had been cancelled.
He will be charged with planning a terrorist act and preparing to travel to Syria, Australian Federal Police Acting Deputy Commissioner Neil Gaughan said.
"We have taken swift action to ensure the safety of the community and we are satisfied that any threat to the community posed by the individual has been mitigated," he said.
The teenager has links to others who are already before the courts on terror-related charges, he said.
His arrest is not related to raids conducted in Melbourne this morning of properties linked to five men arrested last week and charged over a plan to travel by boat to Indonesia in a bid to join the ISIS.