University student Marco Tapia, 23, died as the unintended target of a break-in shooting in Sydney's southwest on September 1.
Two boys, 14 and 16, were arrested on Wednesday and will remain behind bars until they next front a children's court on November 13.
Neither applied for bail on Thursday.
Authorities allege they were involved in the preparation and clean up of the killing.
NSW Homicide Squad commander Joe Doueihi said the boys were identified early in investigations after allegedly leaving a trail of evidence.
"It wasn't very difficult for us to locate them," he said.
"The 14-year-old offender, as he (allegedly) attempted to burn the kill car, burnt himself in the process and ended up in hospital.
"They were, if I can use the word, very clumsy in what they did."
The boys are not alleged to have entered Mr Tapia's family home in Glen Alpine. For that, three suspected offenders remain at large.
But the teens were still charged with murder for allegedly playing a role in a joint criminal enterprise, Detective Superintendent Doueihi said.
Police allege the pair staged vehicles, provided the gunman's weapon and cleaned the home at the centre of the operation.
Sydney's underworld masterminds, often acting from overseas and beyond the easy reach of law enforcement, have over the past half-decade favoured contracting out crimes, often to young, inexperienced agents.
Naive boys, lured by thrills and the financial incentives, were being targeted for the work, Det Supt Doueihi said.
The two charged teenagers, who legally cannot be named, were arrested from homes in Fairfield during two raids on Wednesday.
They were charged with murder, participating in a criminal group contributing to criminal activity, possessing an unauthorised prohibited firearm and two counts of taking a car without consent.
Premier Chris Minns said his thoughts remained with Mr Tapia's family.
"I can only imagine to have a son who's done absolutely nothing wrong, living his life and being murdered in his bed," he said.
"The age of the people who have been accused of these offences is worrying for everybody."
The government on Thursday introduced to parliament legislation cracking down on contract crime.
Opposition Leader Kellie Sloane labelled the arrests deeply shocking and concerning.
"It is no wonder that people in Sydney's southwest and west are frightened and I don't blame them," the eastern suburbs MP said.
Mr Tapia's parents, Sergio and Claudia, described the traumatic experience of witnessing their son's death during an interview with Nine's A Current Affair program on Monday.
Both were at home at the time of the shooting, along with their daughter.
"I remember him taking the last breath," Ms Tapia told the program.
"Hate came to our house."
A GoFundMe fundraiser for Mr Tapia's family has grown to more than $60,000.
Mr Tapia's death was Sydney's first of two suspected mistaken identity shootings in as many days.
Joshua Macdonald, 40, was shot dead at a Merrylands West home, in the city's west, about 3.15pm on September 2.
He had arrived at the home as a visitor minutes earlier, along with a second male and two children who were inside at the time of the shooting.
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