The Northern Territory's Country Liberal Party government on Sunday announced a ban in line with Queensland, the first state to outlaw the therapy.
NT Health Minister Steve Edgington said the government was barring the treatment for under 18s, saying children should be safe from "dangerous ideologically driven practices".
Puberty blockers are medications that short-circuit production of the sex hormones oestrogen and testosterone in adolescents, stalling changes such as the start of periods, hair or breast growth and voice changes.
In October, Queensland's Liberal National Party government reinstated a ban first imposed in January, just hours after it was overturned by a landmark court ruling.
Mr Edgington said public access to puberty blockers in the NT would end for children under 18, in line with Queensland, New Zealand and several European countries.
"Territory kids deserve to grow up free from these dangerous ideologically driven practices with irreversible consequences," he said in a statement.Â
The ban would affect a "handful of teenagers" who had been accessing the drugs through the public-health system, Mr Edgington said.
The minister's ban announcement is a shift from his position in March when he said no changes were being considered.
Eloise Brook, the chief executive of the Australian Professional Association for Trans Health, said the biggest risk to trans children globally were blanket bans.
"The Northern Territory has simply fallen in line with the Queensland ban, making the same mistakes, the same assumptions and ignoring the same kind of evidence that experts have been putting forward," she told AAP.
But Dr Brook said Queensland and the NT would remain outliers as there was no indication other jurisdictions would also impose bans.
NT shadow attorney-general Chansey Paech said the government had chosen to single out a vulnerable group, turning their care into a political battleground rather than treating them with dignity and respect.
The Queensland government extended its ban on Friday, with Health Minister Tim Nicholls saying the pause would remain in place until the results of a UK trial were known in 2031.
The decision coincided with the release of an independent review by Professor Ruth Vine, which found the evidence base underlying hormone therapy was limited and there was a lack of evidence on long-term risks or benefits.
Earlier in December, medical professionals, academics and union representatives were among 415 signatories to an open letter urging the Queensland government to reinstate hormone therapy.
Jemma Clifton of LGBTIQ+Health Australia said puberty blockers were a safe and often lifesaving intervention that gave young people "time to explore who they were with professional guidance".
Sex Discrimination Commissioner Anna Cody said banning puberty blockers would cause significant distress to trans and gender-diverse young people, their families and carers.
"Denying access to this care risks real and lasting harm," she said.
"These decisions are not abstract, they affect the lives, mental health and safety of young people who are already among the most vulnerable in our community."
Dr Cody said she was concerned the Queensland government was ignoring the findings of the Vine review, saying it did not recommend a blanket ban on puberty blockers.
Following the reinstatement of the Queensland ban, the LGBTI Legal Service flagged further legal action to restore the health care that trans and gender diverse young people needed.
Justice Peter Callaghan overturned the initial ban after finding Queensland Health executives were given just 22 minutes to consider the directive to pause puberty blockers.
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