Dr Jo Inkpin in southern Queesland said the Church should shift its attention towards listening to transgender people experiencing shame and depression, and helping them heal.
She told ABC News in Australia: "The Christian gospel in its roots is inclusion, valuing the marginalised and Jesus doing extraordinary things with ordinary people; that's how God has always worked.
"Transgender people enlarge life and our understanding of spirituality and justice and the nature of God and Christian community... we can offer our truth... but it's helpful if other people allow us to do it."
Dr Inkpin, who was born as male but now identifies as female, said it was around the age of four when she began to feel aware of her "true sense of self".
She decided not to publicly declare her transgenderism until last summer, by which time she was in her mid-50s and had been married to a woman, Rev Penny Jones, for more than 30 years.
Dr Inkpin, who grew up in a rural northern England, feared being rejected by the Church and her loved ones over her transgenderism, but claimed it was not her own choice or something she takes lightly.
Explaining the complex medical process many transgender undergo, she added: "If it wasn't something in the deepest part of you, who would do it if you didn't have to?
"But when I took hormones for the first day, I don't think it was just psychological; I just felt for the first time I was comfortable in my own skin."
While the Archbishop of Brisbane Dr Phillip Aspinall, expressed support for Dr Inkpin's announcement, the governing body of the Anglican church in Australia later published a report of gender identity saying "attempts to undergo gender transition are opposed to Christian teaching".
It also concluded that "biological sex is an objective biological fact which cannot be altered at will".
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