Her review of gender care services for under-18s, published in 2024, was commissioned by NHS England after it saw a sharp rise in referrals for patients questioning their gender.
Her report said the evidence around medical interventions in gender care was “remarkably weak”, and there was a lack of research available.
The guidance also says there are “no exceptions” for single-sex facilities at schools and colleges, including toilets and changing rooms, with single-sex sports also protected.
But schools have been given some flexibility over how they deal with issues such as children’s names and uniforms.
The BBC understands single-sex schools will continue to follow the current admissions code, which allows them to admit pupils only on the basis of their biological sex.
Cass said the guidance was “practical and reflects the recommendations of my review, giving schools much-needed clarity on their legal duties so they can support children with confidence”.
Overall, the new guidance also makes a clear distinction between a child’s wishes, and what might be in their best interests.
There is a reminder that while some children explore different gender identities, most do not go on as adults to fully transition to a different gender from their biological sex.
“What comes across quite strongly in the guidance is that proceeding with a social transition is going to be very much the exception, rather than the rule,” Cass told the BBC.
She emphasised the importance of involving parents wherever possible, saying “children don’t thrive well when there are secrets between them and their parents”.
“Too many times during my review I heard about schools having socially transitioned young people without involving parents, and parents were in possession of all sorts of knowledge about what’s going on that the school just wouldn’t know about,” she said.
Education Secretary Bridget Phillipson said the new guidance would deliver “pragmatic support for teachers, reassurance for parents, and above all, the safety and wellbeing of children and young people”.