Staff say cannot provide the level of support required due to the lack of preparedness in schools and colleges.
On Tuesday, members of the Association of Teachers and Lecturers (ATL) have proposed better training and leadership on gender identity in schools in a move widely welcomed by LGBT charities.
Dan*, a trans teacher at a school in Newcastle, said that there was a "knee-jerk" reaction from staff when a pupil faced issues of gender identity.
He said: "Staff panicked. There was a knee-jerk reaction to treat it as a safe-guarding issue, which is completely inappropriate.
"Staff want to help but they’re unprepared so feel nervous. There is no procedure in place.
"Teachers don’t know what advice and information they should provide.
"I advised which websites they should tell the student to use. But they had to be unblocked.
"Lesbian, gay, bisexual and transgender are all classed as inappropriate words by school firewalls."
Another teacher, John*, said that despite his school being inclusive, a lack of understanding of trans issues continues to present issues.
He said: "There’s a gaping hole with trans issues. LGB has been at the forefront – bringing the ‘T’ in is the next step. Homophobia is high profile but transphobia has less visibility.
"Staff are eager for guidance. Schools need support to get the language right and put signposting in place."
And school facilities such as toilets may need to be changed to serve trans students.
History teacher Julia Neal told the London Evening Standard: "If there is gender fluidity they need to understand the importance of gender-neutral facilities."
Appearing on ITV's The Agenda, Labour's shadow education secretary, Lucy Powell, said: "If you know anyone who is transgender they have had a life of being marginalised, being ridiculed, being bullied, being discriminated against.
"And they don't do that out of choice...it is who they are, it is what they feel.
Powell said she would like to see education on transgender issues "as part of a PSHE curriculum - everything from sexting to internet safety and radicalisation but also absolutely about LGBT issues."
Susie Green, CEO of Mermaids trans children's charity welcomed the recommendations for training for schools.
She told The Huffington Post UK: "At one per cent of the population, a school with 1,000 pupils may have around 10 children dealing with issues around their gender, even if they are not visible.
"Trans youth are more likely to leave school early and to suffer abuse at home and in the streets. They are vulnerable, often isolated and stigmatised by the wider community."
Trans youth are more likely to leave school early and to suffer abuse at home and in the streets.Susie Green, Mermaids charity
A spokesperson for Stonewall, the LGBT charity, told HuffPost UK: "The effect that a lack of training and understanding can have on trans young people is serious and distressing. It leaves them vulnerable to victimisation, or to hide who they really, which is extremely damaging.
"Research from Metro Youth Chances shows that 83 per cent of trans young people say they have experienced name-calling and 35 per cent have experienced physical attacks. Over a quarter (27 per cent) of trans young people have attempted suicide. This situation is totally unacceptable."
This situation is totally unacceptable.Stonewall
Dr Mary Bousted, general secretary of the ATL said: "We welcome increased discussion around gender identity and want to support young people, but that requires well-trained teachers, delivering well-informed and inclusive Sex and Relationships Education."
We are also investing £3million in projects to help schools learn how to better deal with homophobic, biphobic and transphobic bullying.Department for Education
A Department for Education spokesperson said: "Every child should feel able to reach their full potential and we know there are thousands of brilliant teachers creating supportive and inclusive environments for their pupils. We already provide advice to help schools understand how the Equality Act affects them, including specific guidance on trans issues.
"We are also investing £3million in projects to help schools learn how to better deal with homophobic, biphobic and transphobic bullying. Sex education is compulsory in all maintained secondary schools - we are clear that it should be relevant to all pupils, and sensitive to their needs."
*Names have been changed