The Glennie School, an Anglican institution in the state of Queensland, confirmed the news via an email to mums and dads at the weekend.
In the message, which was seen by the ABC Brisbane, the private school's headteacher Kim Cohen said: "In our Middle/Senior years, we have a young girl who was born into a boy's body.
"I know this is a concept many of us may struggle to grasp, but please take time out to think about how much harder it must have been for her to make the realisation.
"As a Christian school where we strive to live by the teachings of Jesus, I believe our job is an easy one - we accept those we perceive as different to us, we treat them with the same respect, integrity and compassion that we do all members of the community, and we do so with love."
Local transgender Anglican priest Jo Inkpin congratulated The Glennie School - which is in the town of Toowoomba - saying she was "so proud".
But one Facebook user wrote "[I] feel sorry for those parents that wanted an all-girl school for their daughter(s]", while another said "so much for being a girls' school... we had our hearts set on Glennie... but now seeking alternatives"
A spokeswoman for the Alliance of Girls' Schools Australasia told Daily Mail Australia: "Many girls' schools have had transgender students enrolled and each considers very carefully what will be best for the student and the school community."
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