Both 16-year-olds pleaded not guilty in Children's Court via video link on Thursday after being charged with the murder of Dr Ashley Gordon.
Dr Gordon, 33, died after a confrontation with two teenagers who allegedly broke into his house at Doncaster in Melbourne's east in January.
The role of a third child was also examined in the hearing.
That youngster previously said he had entered Gordon's house but was not there when the GP was stabbed.
Prosecutor Peter Pickering was granted the right to compulsorily examine the boy after his lawyer said the move would be "prejudicial".
Mr Pickering said the two accused boys showed a friend "a bloodied knife" in the aftermath of the alleged killing.
"He's admitting being in a house at a certain time ... but then effectively runs away and hides," Mr Pickering said.
Mr Gordon was found on Eildon Street in Doncaster about 5.30am on January 13 by police responding to reports of an aggravated burglary at his Sargent Street home.
They allege Dr Gordon was involved in a confrontation where he was injured and died at the scene.
The two boys were charged with aggravated burglary, theft and murder after being interviewed by detectives.
They are accused of entering Dr Gordon's Doncaster unit with intent to steal and knowing Dr Gordon was home, charge sheets revealed.
The documents allege the stole a pair of Nike Air Force shoes, Astro A50 headphones, a gaming computer and gaming laptop, a blue Louis Vuitton wallet with ID and bank cards, and keys to a Mitsubishi Triton, with a NXP tag, valued at $5000.
There was no application for bail and the matter has been fast-tracked to the Supreme Court on June 14.
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