Dr David Mackereth said he was sacked from his job for refusing to identify clients by their chosen gender instead of their biological sex.
The tribunal ruled that his Biblical view was "incompatible with human dignity".
The ruling stated: "Belief in Genesis 1:27, lack of belief in transgenderism and conscientious objection to transgenderism in our judgment are incompatible with human dignity and conflict with the fundamental rights of others, specifically here, transgender individuals.
At proceedings in July, giving evidence, Dr Mackereth had said that he was asked in a conversation with his line manager: "If you have a man six foot tall with a beard who says he wants to be addressed as 'she' and 'Mrs', would you do that?"
Dr Mackereth, who now works as an NHS emergency doctor in Shropshire, said that in good conscience he could not do this and said that his contract was subsequently terminated over his refusal.
According to Christian Concern, which is giving the doctor legal support, he told the tribunal he was suspended the following month after being "interrogated" by his boss for refusing to "call any six-foot-tall bearded man 'madam' on his whim". The medic claims he was told he was "overwhelmingly likely" to lose his job unless he agreed.
Dr Mackereth left his role on 25 June 2018, after an email exchange with his boss in which he was instructed to follow the "process as discussed in your training".
He gave evidence that he did not resign his position and was the victim of direct discrimination and harassment.
Andrea Williams from Christian Concern told Premier the ruling was a "crushing of Christian beliefs".
"Dr David Mackereth for almost 30 years has been working in A and E, loves his patients, and treats all patients," she said.
"Dr Mackereth was gentle. He would have called a person by their chosen name. What he couldn't do was put on a form that a biological man was a biological woman, or a biological woman was a man."
Responding to the judge's ruling, Dr Mackereth said: "I am not alone in being deeply concerned by this outcome. Staff in the NHS, even those who do not share my Christian convictions, are also disturbed as they see their own freedom of thought and speech being undermined by the judges' ruling.
"No doctor, or researcher, or philosopher, can demonstrate or prove that a person can change sex. Without intellectual and moral integrity, medicine cannot function and my 30 years as a doctor are now considered irrelevant compared to the risk that someone else might be offended."
Dr Mackereth said he will appeal in order to "fight for the freedom of Christians".
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