The 14-year-old, who was referred to the UK’s only youth gender identity clinic in October 2019, has been told he may have to wait at least another year to be seen.
He said he was experiencing “fear and terror” while he waits for treatment.
Young people are currently facing “extensive waits” to see a therapist, with the average delay being 18 months or more, according to the Good Law Project, which is representing the boy.
The not-for-profit organisation said the health service was legally required to ensure patients referred to gender identity development services (GIDS) are seen within 18 weeks.
NHS England said there had been a 500 per cent increase in the number of young people referred to GIDS since 2013, and that a review was under way.
The service, which is run by the Tavistock and Portman NHS Foundation Trust, provides support to people under the age of 18 who experience difficulties related to their gender identity.
The trust’s adult service, the gender identity clinic, said it was currently offering appointments for people who were referred in September 2017, resulting in an average waiting time of between 33 and 36 months.
Gender clinics for adults across the country have reported similar delays, with the Devon Partnership NHS Trust reporting “lengthy waiting times” while the Cumbria, Northumberland, Tyne and Wear NHS Foundation Trust said patients were facing delays “in excess of 32 months” for an initial appointment and 62 months from referral to treatment.
Trusts have blamed a surge in demand as well as reduced capacity, including staffing problems.
The teenager involved in the case said in a statement: “The length of the NHS waiting list means the treatments which are essential for my well being are not available to me.
“By the time I get to the top of the list it will be too late, and in the meantime I suffer the fear and terror that gender dysphoria causes, every day.”
Gender dysphoria is when a person feels a sense of unease because of a mismatch between their biological sex and their gender identity.
The NHS announced in September that an independent review into GIDS would be carried out.
An NHS England spokesperson said it would include ”how and when“ young people are referred to specialist services.
Jolyon Maugham QC, director of the Good Law Project said: ”Whatever your views about the right treatment regime for young people with gender dysphoria, it can't be right that they face lengthy waiting lists - on some reports up to four years - for a first appointment.
“Children are losing the opportunity to be seen within a window in which they can secure effective treatment and so are, in practice, being denied access to that treatment.”
An NHS England spokesman said: “There has been more than a 500 per cent rise in the number of children and young people being referred to the Tavistock's gender identity service since 2013, as more people come forward for support and treatment.
“The NHS has already asked Dr Hilary Cass to carry out an independent review, including how and when children and young people are referred to specialist services, so legal action against the NHS will only cost taxpayers' money and not help the actions already under way.”
Additional reporting by agencies.