Chol Achiek, 12, and Dau Akueng, 15, died after being attacked at Cobblebank in Melbourne's outer northwest on September 6.
The youths were ambushed by a group of masked males armed with machetes and other bladed weapons.
Police raided properties in seven suburbs across Melbourne's north and west early on Friday morning, arresting seven teens and interviewing them over the alleged killings.
A Thornhill man, 19, a Sunbury boy, 16, a Hillside boy, 15, and a Sydenham boy, 16, were later charged with Dau's murder.
Police charged a Caroline Springs man, 19, a Wollert man, 18, and a 16-year-old Sydenham boy over Chol's killing.
Prince Conteh, 19, Peter Addo, 18, and Abel Sorzor, 19, all faced Melbourne Magistrates Court on Friday.
They were remanded in custody and will return to court on December 12.
The underage accused, who cannot be named for legal reasons, also appeared at a children's court on Friday.
The four did not apply for bail and were remanded in custody before their next appearance on February 18 after prosecutors asked for 16 weeks for police to compile their evidence.
The magistrate granted the timeline, noting the "complexity of the investigations" with the number of accused.
Lawyers for several of the accused said the boys held safety concerns regarding a unit within youth detention and one had nut allergies and needed medication for asthma.
Before they were led away, the magistrate explained to each of the accused the process before their next court appearance.
"Police have asked for some time to prepare evidence. These include statements, videos, it could be a lot of info ... it could take time," he told one of the boys.
Earlier on Friday, Victoria Police Assistant Commissioner Martin O'Brien said the arrests were the result of almost two weeks of diligent and thorough police work.
"The word senseless has been used so many times already in relation to the deaths of Dau Akueng and Chol Achiek, because the reality is that it doesn't make sense," he said.
"Two children walking home after playing sport, who should have had decades of their lives ahead of them.
"Instead, their devastated families are grieving their loss and all the things they will never get to see two children grow up to achieve and experience."
Detective Inspector Graham Banks previously said the attack had the "hallmarks of a youth gang crime".
Neither of the victims were gang members, police said.
The 15-year-old's father, Elbino Akueng, said his son "was a basketball player, not a criminal".
A GoFundMe page set up after the deaths said Dau grew up in the flats around Fitzroy and Collingwood, playing and refereeing for the Collingwood Basketball Association.
He also played for the Wolfpack Basketball Club after his family moved to the city's outer west, while Chol was a member of the Nile Warriors Basketball Club.
Chol's father, Chuti Ngong, told mourners at a vigil his son was a peaceful boy who was loved by everybody.
CCTV footage from the scene showed a group of three males chasing a boy and attacking him on the ground, with his screams calling a woman to his aid.
The impact of the boys' deaths has been felt across the Victorian community, police said as they increased patrols in the area.
The Victorian government reconvened a South Sudanese Australian youth justice expert working group in response to the deaths.
The arrests were a "good thing" after almost two weeks of "excruciating pain" for the victim's families, Victorian minister Lily D'Ambrosio said.
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