Jan Buterman was removed from the Greater St. Albert School Division's teacher list in 2008 because his sex change was not in line with Catholic values.
He filed a complaint the following year, which the school district successfully challenged before the province's human rights commission.
That decision was overturned by the chief of the commission, which prompted the school district to seek a judicial review.
Justice Sheila Greckol of Court of Queen's Bench dismissed the district's request in a written ruling obtained Friday by The Canadian Press.
She said it is time for a commission tribunal to hear Buterman's complaint.
"Five years have passed since the school board terminated Mr. Buterman. The voluminous and continual retreading of arguments at the commission, as well as this application for early judicial intervention on thin grounds, has served only to delay the hearing on the merits," Greckol wrote.
"Human rights process is not only for the lion-hearted and well-heeled conversant with litigation, but also for the timorous and impecunious — for all Albertans.
"The expeditious resolution of complaints becomes an issue of access to justice; justice delayed is justice denied."
Buterman, who is working on his master's in education policy studies at the University of Alberta, said he was delighted with Greckol's ruling.
He said it is still possible the school district could appeal. And even if the case proceeded to the tribunal, it could be long and drawn out.
He acknowledged there is no guarantee that he will win.
"It has been five years and sometimes it has been very hard to cope," he said. "It is of deep concern to me to be faced with a situation where there are entities that can ignore rights that we all have."
Officials with the humans rights commission and the school district were not immediately available for comment.
In 2011, Buterman turned down a $78,000 cash settlement offer from the publicly funded school district because it would have required him to keep quiet and drop his human rights complaint.
He said he was fired in 2008 despite receiving a letter from the district praising his teaching abilities.
According to the facts listed in Greckol's ruling, a board official wrote Buterman another letter when the district learned he was changing from a woman to a man.
"The teaching of the Catholic Church is that persons cannot change their gender," read the letter that deputy superintendent Steve Bayus wrote after conferring with the Archbishop of the Catholic Archdiocese of Edmonton. "One's gender is considered what God created us to be."
The letter went on to say that the school division was bound by the teachings of the church and that it intentionally hired teachers who were models of those teachings.
Bayus wrote that Buterman's sex change was not aligned with the teachings of the church and would create confusion with students and parents.
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