The mother claimed victory after the Queensland government's ban was overturned in the Supreme Court on Tuesday, saying it brought an end to a harrowing ordeal.
However Health Minister Tim Nicholls confirmed hours later that he would issue a ministerial direction that will restore the puberty block pause in Queensland.
The mother's devastated supporters on Tuesday night said they would discuss their legal options.
The mother, who cannot be named for legal reasons, launched the historic challenge against the government after it halted hormone treatment for transgender children.
She did not hide her relief after Supreme Court Justice Peter Callaghan set aside the ban in a judgment delivered on Tuesday.
"This has been a harrowing and traumatising ordeal," the mother said through her lawyer.
"I'm incredibly relieved it is over and that justice has been achieved by my child and the other young people affected by this ban."
Justice Callaghan overturned the ban after finding Queensland Health executives were given 22 minutes to consider a directive that would ban hormone therapy for young people.
"My child's medical treatment was ultimately decided by the government with no input from anyone with expertise in treating transgender young people," the mother said.
"I don't know any Queenslander who would want decisions about their child's medical care decided by politicians or doctors operating outside their area of expertise."
The case was based on whether Queensland's health service made an independent decision with proper public consultation to halt puberty blockers.
"The only way that was argued that (the Queensland Health CEO) complied with this requirement is by reason of a videoconference which lasted for about 22 minutes," said Justice Callaghan who ordered Queensland's health service pay the mother's legal costs.
The judgment did not establish the merit or otherwise of puberty blockers.
Mr Nicholls late on Tuesday confirmed the ban would be reinstated via a ministerial direction.
"The Supreme Court was concerned with the circumstances of the making of the directive, not whether a pause ... was appropriate," he told parliament.
"I'm satisfied it is appropriate and in the public interest that I issue a written ministerial direction to all Hospital and Health Services with immediate effect."
The ministerial direction to ban puberty blockers would not affect people who were already on a treatment plan, he said.
"As parents, as communities and as a state, we owe it to children to ensure care is grounded on solid evidence and we act with caution," Mr Nicholls said.
The mother's supporters said the state government may have opened itself up to a legal challenge with its latest decision.
"It's deeply disappointing that the minister is threatening to double down on a policy that has already caused so much harm," Equality Australia Legal Director Heather Corkhill told AAP.
"The government could also be back in hot water by opening itself up to a further legal challenge."
Mr Nicholls' ministerial directions must be backed by evidence that they are in the public interest, she said.
"That means promoting public health and safety, improving service quality, and protecting vulnerable people," she said.
"Denying young people access to evidence-based, safe and effective healthcare does none of those things.
"It's also incredibly offensive for the government to suggest that parents can't be trusted to make the right medical decisions for their own children."
Queensland was the first Australian state to ban hormone treatments for children diagnosed with gender dysphoria, following claims puberty blockers had been given to kids as young as 12 without authorised care.
Under the ban, hormone therapies are no longer accessible to new patients aged under 18 as the government awaited a review into the treatment.
The review into hormone treatment for children with gender dysphoria was due to provide a final report by the end of November.
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