The Northern Territory's only LGBTQI health clinic is a step closer to providing adequate healthcare for teenaged transgender patients.

Transgender teen Brody Martin was among the first to undergo long-awaited hormone therapy at the clinic on Friday, following a family court ruling that meant doctors could administer hormone therapy themselves.

The 17-year-old began experiencing gender dysphoria in 2014, and seriously considered transitioning later the following year.

"I've been trying to go to different doctors and stuff for about two and a half years now, so it's been a very long wait, and it's relieving to finally do something," he said.

"They've been saying you have to wait until you're 18 or go through the family court, and that costs lots of money and lots of time."

Dr Danielle Stewart runs the self-funded monthly LGBTQI health clinic out of her private practice in one of Darwin's coastal suburbs.

Dr Danielle Stewart, who specialises in LGBTI health, in her clinic room in Darwin. ( ABC Radio Darwin: Emilia Terzon )

She estimates transgender people made up about 80 per cent of the clinic's patient base.

"People coming to our monthly clinic who are under 18 no longer have to go through a complex process of psychiatric assessments, endocrinology appointments and then legal court battles," she said.

Following Thursday's ruling, the clinic can now centralise its services into a 'bigger picture' of transgender health.

This means doctors can now administer hormone therapy alongside the clinic's existing services instead of deferring to court-approved endocrinologists with potentially little expertise in gender diversity.

"The truth is this is a complex area of health and the benefit to those individuals of being able to sit and discuss these issues with someone who really knows what they're talking about is critical," Dr Stewart said.

Darwin's dire track record put lives at risk

A sense of helplessness among Darwin's transgender population compelled Dr Stewart to open the monthly service in mid-2016.

Since then, the clinic has expanded from one day a month to two — with a possible third in sight — with a growing popularity that Dr Stewart links to a lack of information and services.

Dr Stuart Aitken, one of a rotating stable of sexual health specialists who are paid to fly up and attend the clinic, said Darwin lagged behind Australia's other major cities.

A sign for a LGBTI specialist medical clinic day in the lobby of a Darwin health practice. ( ABC Radio Darwin: Emilia Terzon )

"You really do notice quite a few gaps in service provision for transgender people up here in Darwin," he said.

He said the arenas of mental health and psychiatric help were especially lacking.

"And that lack of service directly translates into health disparity," he said.

"It explains most of the gap in the life expectancies and suicide rates for transgender people. That actually translates into early death, disability and disease."

'Excited, overwhelmed' at court ruling

Hours before receiving his first shot of testosterone, Brody said the delay in access would ultimately make puberty's changes harder to undo.

"It would've been nicer to go onto the hormone blockers before puberty and go straight into the correct puberty, but it's just a relief it's happening now," he said.

Nonetheless, he was "excited, overwhelmed and shocked" by Thursday's ruling, delivered to him during his Year 12 formal.

"I could not wait to ring Brody and let him know of the good news," his mother Cindy Reid said.

"When I did ring, he broke down in tears."

Dr Stuart Aitken says there are significant gaps in transgender health provision in Darwin. ( ABC Radio Darwin: Jesse Thompson )

Dr Aitken said there was already a queue of other young transgender people and their families contacting about hormone therapy should careful assessment deem them suitable candidates.

Asked if the court ruling would mean a busy few months at Dr Stewart's clinic, she said she was not sure.

"I'd like to think so but I don't know. I think the reasons that it can be difficult for people to come and discuss these issues and seek help are very complex," she said.

"It's a huge thing to consider in your life, in your family and as a school kid. These are big things."