The NHS gender identity service is seeking leave to appeal against a High Court ruling that restricts children under 16 from accessing "puberty-blocking" drugs.
The NHS service says the move harms young people with gender dysphoria.
Doctors and parents have told the BBC the ruling could put already vulnerable trans teens at risk.
And trans young people have been giving their reaction, with one calling the ruling "honestly terrifying".
Gender dysphoria is when a mismatch between a person's sex assigned at birth and their gender identity causes them distress.
Accessing puberty blockers is currently one of the first steps in treatment for young people wishing to transition.
Earlier this month, three High Court judges ruled that children under 16 with gender dysphoria are "unlikely to be able to give informed consent to undergo treatment with puberty-blocking drugs".
Dame Victoria Sharp, sitting with Lord Justice Lewis and Mrs Justice Lieven, said: "It is highly unlikely that a child aged 13 or under would be competent to give consent to the administration of puberty blockers.
"It is doubtful that a child aged 14 or 15 could understand and weigh the long-term risks and consequences of the administration of puberty blockers," she added.
As a result, trans children under the age of 16 will now need a clinician to apply to the High Court to be able to access puberty blockers, and all current referrals and appointments have been paused.
The BBC understands that clinicians may also seek guidance from the High Court for all trans young people under 18.
The Tavistock and Portman NHS Trust runs England and Wales' only children's gender identity service.
It is now seeking leave to appeal the High Court decision, along with University College Hospitals NHS Foundation Trust and Leeds Teaching Hospital NHS Trust.
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Theo, a 14-year-old trans boy who suffers from extreme gender dysphoria, came out as trans when he was 11. He is still waiting to see a gender specialist, and last year he tried to take his own life.
He wanted to "disappear", he said, after being left to go through female puberty while stuck on a "never-ending" NHS waiting list.
"I felt like I wanted to be dead rather than waiting. I spend a lot of time wishing I could be a normal boy and there is no help for me.
"I have support around me, but my gender dysphoria feels like I'm not me in my own body," he says.
"It can make me really depressed. I hate seeing my body, so I can barely have a shower or a bath."
Theo's mum, Loreto, says that even when Theo was lying in intensive care "connected to pumps and with tubes through his nose", she could not secure him any gender identity help.
"It was a very dark moment, but Theo still hasn't been given any gender support from the NHS," she says.
"I still have a child who can't go outside. I have to constantly check how he's dealing with life, and tell him to focus on the positives."
Responding to the ruling, Theo says he should be able to decide what happens to his body.
Image captionThe NHS Gender Identity Development Service is based at the Tavistock and Portman Trust
"People think that trans kids are lunatics who have no idea what's going on in the world. People think trans kids are just handed medication without any questions asked, but that's not true at all.
"We have to read a lot, we have to ask questions, we have to fight. We're forced to be a lot more mature than most kids I know. This ruling is honestly terrifying," he tells the BBC.
The NHS Gender Identity Development Service (GIDS) website states: "This judgment and the revised NHS England service specifications for GIDS raise a lot of questions and may be the cause of anxiety and distress for our patients and their families/guardians.
"We also appreciate that this comes at a time when our waiting times have never been longer, and amidst a pandemic."
While the NHS gender identity service says that access to any medication will not be "automatically withdrawn" as a result of the ruling, they confirmed that no new referrals are being accepted.
A spokesperson for the NHS Trusts involved told the BBC this is a "temporary pause".
Image copyrightEMMA WILLIAMS
Image captionEmma (left) supports her trans daughter Emily (right) at LGBT Pride events
Emily, a 12-year-old trans girl from Liverpool, was first referred to the Tavistock by her GP in May 2017.
After being assessed over 12 appointments, across two years, involving Emily and her parents, she had just been recommended for puberty blockers by the service.
Emily's mother, Emma, fears her daughter "will not make it through" male puberty. "Emily is running out of time. We will have to figure something out, and fast," she says.
"She's already so uncomfortable in the body she's got, and if it becomes more male, she won't be able to tolerate it."
In October 2020, Emily's NHS psychotherapist wrote: "I am satisfied that Emily, with the ongoing support and guidance of her parents, has a good understanding about the potential side-effects of this treatment."
A clinician who currently works within the NHS GIDS, told the BBC her patients are now being left alone to deal with distress.
"The young trans people I'm talking to now are experiencing deeply distressing mental health problems," she says.
"To be a young trans person nowadays requires a bigger fight than ever, but most of the trans people I see do not have any fight left in them."
The clinician wanted to remain anonymous, because of the backlash that could come as a result of her speaking out.
She says: "I know of several young people who have tried to take their lives, some successfully, and that was before these legal challenges which will only slow down and block our services even more."
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Dr Adrian Harrop, a GP from Liverpool who has defended the right of children to begin transitioning, says trans young people have now had "the rug pulled from underneath them".
"It makes me terribly worried that there is now nothing there for those children, and nothing that can be done to help them.
"Parents are being left at a point where they're having to struggle to cope with these children who are in a real state of distress and anxiety. Sadly, there is a very real risk of seeing more suicides," he adds.
In a letter seen exclusively by the BBC, GenderGP - one of the only private healthcare providers for transgender people in the UK - calls on NHS England's Medical Director for Specialist Services, James Palmer, to take urgent action.
The letter asks him to provide "interim solutions to prevent harm". It adds: "The mental health implications of this cannot be underestimated, and the risk of self-harm and suicide must be acknowledged."
GenderGP is a private company founded by Helen Webberley, who was suspended by the General Medical Council for running an unlicensed transgender clinic. She is challenging the decision.
Clarification and update 23 December: We have made some changes to this article which include amending its opening line to make clear that the NHS gender identity service has not appealed against the High Court ruling but is seeking leave to do so. We have also added a paragraph which provides further background information on GenderGP and included links to the BBC Action Line.