Jamie Love, 17, arrived at Govan High School - which the Daily Mail describes as "notoriously rough" - wearing an outfit of tights, denim shorts, hair extensions and make-up, announcing he wanted to be known as Kierny.
He says that during his first lesson of the day a teacher came to his classroom and took him to the head teacher's office, where, Jamie alleges two deputy heads asked him: "What are you trying to do to this school?" before telling him to get his stuff and "not come back".
The schoolboy - who describes himself as a dancer - says he had been telling his teachers for months he felt "trapped in a boy's body". He says he now feels "betrayed" by the people he trusted.
He told the Mail: "It took me years to finally open up to someone about my sexuality and now I feel betrayed by the people I trusted. I have always felt different but I have never been able to talk about it.
I left the school in tears feeling totally humiliated and embarrassed.
He claims he told the school in advance that he was planning to attend as a girl, something the school refutes. They say he was asked to leave because of his "lack of commitment to education".
Jamie admits he has "behavioural problems" and has been disruptive at school, but says this was in the past and was down to his confusion over his sexuality.
His mother Alison, 45, also insists that her son's cross-dressing was discussed with the school. She says: "Jamie has done nothing wrong here. He has every right to express himself the way he wants and I will stand by him."
Jamie had been in the middle of a hairdressing course in the sixth-form of the school, and was hoping to go on to Central College in Glasgow.
His sister Michaela, 19, said that he should be allowed to dress as a girl if he wanted to as "people turn up to school wearing trackies, trainers and polos and they don't get told to leave."
A spokesman for Glasgow City Council said that Jamie is still on the school roll and has not been expelled, adding: "The suggestion the pupil was told he was not welcome at the school because of his clothing is completely untrue. He did not speak to us about the way he wanted to dress, however, his choice of clothing is not an issue and he was not told it was inappropriate. He was advised on Monday that school was no longer meeting his needs and he should move on, and that staff would continue to support him. However, he appears to want to continue at school."
The spokesperson went on to say that it was important they put "measures in place to accommodate Jamie's choice of clothing" and that the school would like to meet with him and his mother and "relevant support agencies" so he can "come back to school in a positive and supportive climate."
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