Lily Madigan, 18, identifies as female but was born a male.
She was threatened with suspension from St Simon Catholic School in Kent after being told she was not allowed to wear the female uniform.
The pupil was supported by more than 200 members of the school who signed a petition supporting her.
Ms Madigan hired a solicitor and was told the school had a legal obligation to allow her to wear whatever uniform she chooses.
The school told The Sun newspaper: "We value highly the views of all of our students, and take all points of view into account as we develop."
Philippa, a transgender Christian from the Sibyls support network, told Premier the school needs to be more understanding of what the pupil is going through.
She said: "What you need to do really with young people is give them time to work out who they are and what's the best way of dealing with the way they feel.
"Schools imposing views of this nature are most unhelpful and indeed potentially very damaging."
Philippa went on: "I think it comes back to some misunderstanding that this is either some sort of sexual perversion or some form of lifestyle choice.
"The thinking these days is very much that your gender identity is probably formed in the womb, the way your brain develops."
Gerald Coates is a Christian author on gender and sexuality, and thinks the school is correct, not the law.
He told Premier the rules are there for a reason: "I think there are all sorts of things as children, teenagers and adults, we want, but it's unhelpful, unhealthy and wrong.
"The school is right because obviously there are rules with regard to uniforms and when you send your child to a school, you are aware of those rules."
He told Premier this could have further impacts: "this then brings you to, which toilet do they go into, and on and on you go, and it's a very, very confusing space.
"I think the school were right to say, if you've got male genitalia you'll wear the uniform of a boy, and if you've got female genitalia, you'll wear the uniform of a girl."
Listen to Premier's Hannah Tooley speak to Philippa here:
Listen to Premier's Hannah Tooley speak to Gerald Coates here:
