Solving gender identity issues in children is complicated, and is not always going to be the answer to everything, says NHS England's gender identity development service.
They need help "from all sides", say experts from the London clinic, because many of the under-18s are also dealing with mental health problems.
Referrals to the service have more than tripled since 2014-15 - to 2,590.
Fewer than half decided to have any physical treatments.
The Tavistock and Portman NHS clinic, which was the first gender identity clinic to be set up in the UK, has now been joined by two others in Leeds and Bristol.
Another clinic in Birmingham is also planned.
The clinics all see children and young people experiencing distress over their gender identity, also known as gender dysphoria.
Most are aged 14 to 16, going through puberty, and more than two-thirds are female at birth.
At the clinics, they are assessed with their families in four to six sessions with two clinicians over the course of a year.
The NHS clinics do not provide hormone blockers until the child has started puberty, and cross-sex hormones are only given from around the age of 16.
'A complicated picture'
Dr Polly Carmichael, consultant clinical psychologist and director of the Gender Identity Development Service (Gids), said many had complex social and personal histories.
"We think about all the needs of young people and try and work closely with local services to clearly manage risk around self-harm, and other difficulties, but also to raise awareness around gender issues," she said.
"I think there is sometimes a danger there can be a split - if someone is presenting with issues around their gender identity, that local services perhaps think that's going to be the answer to everything.
"Whereas in reality it's a complicated picture that needs to be addressed from all sides."
Dr Carmichael and colleagues had no explanation for the huge jump in referrals to clinics over the past five years, but said it was likely to be down to greater awareness of gender identity issues and greater acceptance of them.
They also said social transitioning, which means telling family and friends of a gender change without any treatment, had become more popular - but was not something they recommended.
'Wall of reality'
Dr Bernadette Wren, head of psychology at Gids, said it could cause problems for children and young people.
"They are moving into puberty and the young person suddenly faces a kind of wall of reality, and that makes us anxious, we think that's setting up problems."
Young patients currently have to wait around two years to see a gender identity specialist after being referred.
If they have not been seen by the time they turn 18, they should not have to join another waiting list for adult services, the experts said.
Dr Wren said the UK's gender identity development service for children and young people was seen internationally as one of "the most cautious, painstaking and thoughtful".