The 17-year-old male, from Melbourne, entered the plea in Supreme Court on Monday, Xinhua reported.
The teenager, who cannot be identified for legal reasons, was arrested in May after the Australian Federal Police (AFP) raided his home.
During the raid, police confiscated a number of items, including a pressure cooker, suspicious powder as well as nails and screws, which they alleged would form the basis of an improvised explosive device (IED).
Earlier this year, court documents revealed that police had uncovered an encrypted file entitled "Pressure Cooker Backpack Bomb with Switch Detonator and Make a Bomb in the Kitchen of Your Mom" on the teenager's computer.
Police also discovered IS and Al-Qaeda propaganda material in the boy's possession.
The AFP agents believe the boy was planning a suicide attack on Mother's Day, Australia's national day of appreciation for mothers, on May 10, 2015.
Initially, the teen was charged with three counts of terrorism-related offences, but on Monday, the prosecution withdrew two of the charges.
As the boy is under the age of 18, the teen's lawyer had sought to have the case heard in the Victorian Children's Court, a move that was rejected by the judge due to the seriousness of the matter.
He will face the directions hearing in the county court on Thursday next week, according to prosecutors.
The teen did not apply for bail and was remanded in custody.
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