New figures show Childline is receiving a record eight calls a day from children who are unhappy with their gender.
Transphobic abuse prompt children to report suicidal thoughts and mental health issues, Childline says.
Data released by the NSPCC, which runs the helpline, reveals it held 2,796 counselling sessions in 2015/16 with children as young as 11 who felt their biological sex was wrong.
It is more than double the amount of calls Childline received when it first began recording figures on transgender and gender dysphoria issues in 2012/13.
Childline says homophobic bullying and transphobic abuse was mentioned in 450 of the sessions and often prompted children to report suicidal thoughts, self-harming and mental health issues.
NSPCC chief executive Peter Wanless said homophobic and transphobic abuse “can trigger serious mental health issues and crippling shame”.
He said: “It’s vital young people are confident that if they speak out, they will be able to try and navigate these confusing and complex feelings without also having to fight prejudice and abuse.
“Adults must support a child as they explore what they’re feeling and guide them to get the right help when necessary.”
The charity, which runs Childline, said public awareness around transgender issues in recent years had made children more confident to come forward about their feelings.
A 13-year-old girl who identified as a boy said: “I’m being bullied on my social network account about being transgender and it’s awful.
“They constantly send me hateful messages and tell me to kill myself. I think it’s someone at school as they seem to know things about me.”
But critics argued that adults should avoid leading young children who may have doubts into believing that they needed to “change sex”.
Jill Kirby, an author and researcher on the family, said: “We should be concerned at this outbreak of counselling, and taking a hard look at what is being suggested to these children, who may be experiencing different ideas about their identity as part of growing up.
“There is a risk that children may be led into paths that they later regret. We should be particularly concerned at the possibility that counselling children may lead to drug treatment and the dangers that could entail.”