A Sydney teenager charged over an alleged Anzac Day terror plot has pleaded not guilty.

The 16-year-old's lawyer Zemarai Khatiz entered the plea on his client's behalf in the Parramatta Children's Court today.

The teenager was not in court, and Mr Khatiz said he there would be a bail application on Friday, with supporting evidence from a psychologist's report.

The 16-year-old boy, who cannot be named for legal reasons, was arrested near his Auburn home on Sunday on suspicion of trying to get a gun and carry out a terrorist act at an Anzac Day service.

Police swooped after the apprentice electrician allegedly sent messages on an encrypted mobile app seeking to buy a gun, and the date April 25 mentioned.

"Extremist propaganda" was also allegedly found by police at the boy's home.

No weapons or explosives were found during the search.

He first became known to police last May as part of an investigation into a Melbourne terror plot, foiled on the eve of Mother's Day, the ABC reports .

He was said to have been communicating online with senior Australian Islamic State recruiter Neil Prakash.

After the boy's home was raided, he was reportedly signed up to an intervention program jointly run by the Australian Federal Police, NSW Police and Victorian Police.

The program involves psychologists, teachers and religious leaders working to deradicalise potential young terrorists.

The boy is expected to apply for bail today, which police said they will oppose.

During a press conference yesterday morning, NSW Police Commissioner Andrew Scipione said the risk from the particular threat had been "thwarted".

The teenager has been charged with one count of acts in preparation for, or planning, a terrorist act, which carries a maximum penalty of life imprisonment.

Mr Scipione said there was an "online component" to the alleged offences and believed the teenager was acting alone.