He had short spiky hair, hated wearing the school's checked skirt and in Year 12, the Avila College student came out as a transgender male.

"I presented as quite masculine. I didn't fit in. I wasn't going on about boyfriends and about make-up," the 19-year-old said.

"It was inherently a very gendered environment. It made it more difficult."

It's a situation many single-sex schools – whose entire existence has relied on rigid concepts of gender – are grappling with.

For the first time, the region's peak body for girls schools, the Alliance of Girls Schools Australasia, is urging its members to support transgender students.

This includes males who transition to females and want to enrol in girls' schools, and females who transition to males and want to remain in girls' schools.

Earlier this week, the organisation, which predominantly represents private girls' schools, held a conference which focused on gender and transgender issues.

"It's an emerging issue, everyone is still learning what to do and that includes the doctors, the psychologists, the support services," the Alliance's president and Mentone Girls' Grammar principal Fran Reddan said.

"It's critical that we provide a safe environment where all students can express their gender identity."

Micah Scott, the chief executive of LGBTI youth group Minus 18, said single-sex schools faced a unique challenge.

"Their existence is based on the concept that the sex you are assigned at birth will match your gender identity," he said.

He said teachers needed to avoid gendered language like "good morning girls" and should provide more flexible uniform options.

Jeremy agreed, and said he felt very uncomfortable wearing his school uniform.

"A teacher told me that I could wear the trousers but said everyone would look at me funnily," he said. He claimed another teacher picked on him.

But despite these challenges, he also received a lot of support from the Catholic school.

A teacher who suspected Jeremy was struggling with his gender identity emailed him a link to a documentary about Lieutenant-Colonel Cate McGregor, who came out as a woman in 2012.

"She said I think this would be really helpful. That's when I realised I was transgender," he said.

He slowly began to gain more confidence, and in 2014 he confessed to his friends that he identified as male.

While "Jeremy" was emblazoned on the back of his year 12 hoodie, teachers and students still referred to him as a "she".

Jeremy's Year 12 hoodie. Photo: Henrietta Cook

And he wore a suit to his Year 12 formal.

"I was the first person in my year level to wear a suit. I felt so much more comfortable," he said.

Avila College acting principal Christine Kralj said she was pleased that Jeremy was able to speak about the issues associated with being a young transgender person.

Human Rights Law Centre director of advocacy Anna Brown said there did not seem to be a clear protection for transgender students in single-sex schools under federal discrimination law. But she said it was a grey area and yet to be tested in court.

She welcomed the leadership shown by the Alliance of Girls Schools Australasia and said it was consistent with good practice and international human rights standards.

"These support the affirmation of gender identity and accommodate the needs of a vulnerable cohort of young people."

She said schools should let transgender students wear uniforms and use toilets that reflected their gender identity. They should also ensure that sports divided along gender lines are inclusive, and that students are referred to using the name and pronoun of their choice.