The puberty blockers trial has already proved controversial, with campaigners threatening legal action.
Keira Bell, who took the Tavistock gender clinic to court in 2020 after she was given puberty blockers and cross-sex hormones as a teenager, said the trial should be halted immediately. If it is not, she says she and another campaigner will start judicial review proceedings at the High Court.
She said it was "disgusting" that children were being put on the drugs when they had already been banned because they were "unsafe".
In her case, the High Court ruled that under-16s were "unlikely to be able to give informed consent" to puberty blockers, but this was later overturned by the Court of Appeal which ruled that doctors can judge whether young people can give consent to the treatment.
Some clinicians from the Clinical Advisory Network on Sex and Gender, which campaigns for rigorous science and improved treatment options for gender-questioning people, have also questioned whether the trial can be carried out ethically.
Study lead Prof Simonoff said: "We know there are ongoing societal discussions about gender transition, but this research is focused solely on informing and improving healthcare by better understanding how to support the physical and mental health of young people with gender incongruence."
Dr Hilary Cass said she was "really pleased" Prof Simonoff and the KCL team were undertaking the trial.
She said: "My review uncovered a very weak evidence base for benefits from the use of puberty blockers for children and young people with gender dysphoria. In fact, some children had more negative than positive effects.
"However, given that there are clinicians, children and families who believe passionately in the beneficial effects, a trial was the only way forward to make sense of this."
She added: "Although a lot of media attention has focused on the trial, they have a much broader research programme. Following the outcomes for young people who do not elect for a medical pathway will be just as important as following those who do."
A spokesperson for charity Stonewall, which campaigns for the rights of LGBTQ+ people, said all young people should have access to the very best medical care, guided by evidence.
"We urge the government and policymakers to invest in delivering excellent healthcare for trans young people and to make sure the voices of trans young people and their families are at its core."