PM Malcolm Turnbull called a royal commission last year after a TV show broadcast footage of inmates being stripped, assaulted and tear gassed.
Two former inmates are now seeking compensation as part of a group action, said law firm Maurice Blackburn.
They could be joined by hundreds of others, the firm said.
The lawsuit alleges Dylan Jenkings and Aaron Hyde were abused by guards while in the Don Dale Youth Detention Centre. Both are now serving sentences in an adult prison.
Last year, Amnesty International described the regime at the centre as "institutionalised brutality", with teenagers held in solitary confinement with no access to light or water for long periods.
The document, filed in the Federal Court, claims Don Dale staff "struck" Hyde - then aged 15 - in the ribs during an incident in 2012.
They also allegedly "slammed" his head into a door while he was handcuffed, before placing him in an isolation cell for up to three weeks.
"He was stripped naked and he'd been asking for a blanket and a guard told him to masturbate to keep himself warm," his mother, Tracey Hyde, told the ABC.
"That should happen to nobody. Yes, there are kids that are in there for a reason, but that doesn't mean you can treat them like animals."
Don Dale guards beat Jenkings with batons and punched him twice in the back of the head, according to the claim.
Jenkings claims he was then locked in a cell for 48 hours.
Maurice Blackburn lawyer Ben Slade said: "No-one denies these kids may have broken the law, but they didn't deserve to be broken by the law."
"They have the same right as anyone else to seek compensation through the courts for the harm and deprivations inflicted upon them."
The class action could include anyone subjected to assaults, threats or unreasonable isolation while in Northern Territory youth detention between August 2006 and December 2016, the firm said.
The royal commission is scheduled to hand down its final report on 1 August.
Australia's Northern Territory government is facing a class action lawsuit over the alleged abuse of youths in detention.