Dr Adam Tomison announced his resignation as director-general of the problem-plagued department on Monday, seven years after taking the top job.
"This has been a difficult decision but now is the right time for me professionally and personally to resign from Justice and consider new opportunities," he said in a statement.
While he was a recognised expert in the prevention of child abuse and family violence, his time at the department's helm has not been without controversy.
"By far the most difficult challenge of my career has been youth detention and managing the complex cohort of young people who emerged post-pandemic with a level of violence and destructive behaviour not previously seen," he said.
The embattled Unit 18 facility was built last year at Perth's Casuarina Prison under Dr Tomison's watch, with him describing it as a "short-term" facility to house high-risk juvenile offenders.
Sixteen-year-old Cleveland Dodd was incarcerated in Unit 18 when officers found him unresponsive in his cell in the early hours of October 12, after he had twice contacted guards through the intercom, threatening to hurt himself.
He was taken to hospital in a critical condition, where he died.
The teen is the first child to die in juvenile detention in WA since records began.
An interim report by the justice department into his death found multiple system failures, including that he was not placed under heightened-risk observation despite making self-harm threats, and a staff member checking inmates was not carrying a radio.
The boy was held in a damaged cell and its closed-circuit camera was covered in toilet paper obscuring its view, while two of five staff required to wear body-worn cameras had not signed them out.
The investigation also found staff were watching movies in the control room at the time Cleveland self-harmed and the senior officer on duty had unbuttoned his shirt and removed his boots and belt as he "rested" in a darkened nearby office.
The coronial inquest into Cleveland Dodd's death has been fast-tracked and will get underway  in April.
WA Attorney General John Quigley said Dr Tomison played an integral role in improving the justice system.
"Dr Tomison's knowledge and experience in the justice and criminology sectors have been invaluable in overseeing the department, and indeed his leadership during the pandemic was exemplary," he said in a statement.
"I thank (him) for his outstanding contribution and wish him all the best for the future."
WA Corrective Services Minister Paul Papalia also thanked Dr Tomison for his leadership in the challenging role, saying he didn't take the responsibility lightly.
He will remain in the role until January.
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