Other parents were not told, just as they would not be told about other measures taken to support a child, he said.
"I believe our parent community supports diversity [anyway]. It's a child who identifies as a different gender than the one they were born with.
"There's nothing scary about that, there's nothing unusual about that. It's been happening since the beginning of human kind. We are just more aware of it now, and we're making sure [those transitioning] are safe.
"I'm proud to be part of a school that says 'it's okay to be who you are and we are going to make sure you get the best education, without worrying about anything else'."
Duncan Matthews from Rainbow Youth applauded the school.
"It is awesome the school has taken active steps helping those people who wouldn't feel comfortable using a gender-specific bathroom," he said.
"It is great this school is leading the way to show other schools the sky doesn't fall down if you have a gender-neutral or unisex bathroom."
A recent youth survey revealed 1.2 per cent of New Zealand school-aged children identified as transgender - more than 3000 in Auckland and more than 9000 nationwide.
It is not known how many primary-age children are transgender and the ministry said it did not keep such figures.
A research project in America in 2014 stated children become aware of their gender identity by age 3 to 5, and a report in the UK yesterday said children as young as 3 were being treated at gender transition clinics.
Matthews said the dilemma of which bathroom to use was huge for transgender children.
An increasing number of parents were seeking support and advice for their young transgender children, Matthews said. He fielded about two calls a month from parents struggling because their school wasn't supportive. Issues included gender-specific uniforms or teachers unsupportive with name changes.
"Some children leave that school and start at a new school with their preferred identity, especially if the previous school is not supportive."
Katrina Casey from the Ministry of Education said unisex bathrooms were becoming common at schools and there were no separate boys and girls toilets in new builds.
"Our standard design is for individual self-contained bathrooms that can be used by either gender," she said.
Casey said unisex toilets made good sense as "they're versatile."
Last year the ministry revised sexuality education guidelines which included the suggestion of gender-neutral uniforms and a review of toilet spaces.
Earlier this year, two Wellington secondary schools decided to fit gender-neutral bathrooms for students who felt uncomfortable using "male" or "female" bathrooms.
Wellington High School has already transformed its boys' bathroom into gender-neutral facilities and Onslow College is about to do the same, spending thousands of dollars to convert an old block of girls' toilets.
• For support and advice contact Rainbow Youth www.ry.org.nz or (09) 376 4155
