One survey in 2014 found that a third of transgender children had skipped class because they feared discrimination.
Bullying is a big problem, mainly by fellow pupils but sometimes by teachers, too.
Susie Green, the chief executive of Mermaids, says that around half of schools fail to help pupils when they come out as transgender.
In some cases, teachers refuse to take actions as simple as accepting a new name.
In 2010 the Labour government passed an equality act that obliges public and private institutions not to discriminate against transgender people.
That has led to some improvements.
Uniforms increasingly have a unisex option.
New schools tend to be built with cubicle toilets and changing rooms, rather than communal ones split by gender.
Whereas America has national debates about toilet use, in Britain discontent rarely spreads beyond local parents.
Still, most schools face up to the issue only when one of their pupils comes out as transgender.
Even when well-meaning, a rushed response can make things trickier.
Teachers are sometimes reluctant to discuss the subject for fear of saying the wrong thing (at St Paul's, pupils came up with a glossary to help) .
Yet, say campaigners, most of the time teachers need only listen to what children want.