Principal Sandy Hastings said the school removed gender from its uniforms in 2016.
The gender neutral uniforms made students more comfortable and allowed them to do more activities.
"Swinging upside down on the bars is never any fun in a dress, for anyone," Hastings said.
She said the school had gender neutral bathrooms for both staff and students. Its library was building its catalogue of books with diverse characters.
"The students often see diversity as part of their normal. That is certainly our goal," Hastings said.
She said the school's community was accepting of the changes. Many parents had specifically chosen Beckenham Primary School because of its inclusive practice.
"Our children are wonderful educators. Their inclusion and willingness to embrace diversity is taken into the homes they live in and shared with the adults who raise them, resulting in some really powerful, positive conversations," Hastings said.
A 10-year-old transgender primary school student, who asked not to be identified, has decided to keep her biological sex to herself. She said if she was to tell everyone in her school community she would face discrimination.
"Some people might be mean about it," she said.
Her mother, who also asked for anonymity, said schools were improving slowly but still had a long way to come.
She said her daughter's "dead name" (name given at birth) had come up on a test recently, leaving her feeling ashamed.
"What if that was to happen further down the track in NCEA exams? It's just not right."
The Ministry of Education's policy deputy secretary, Dr Andrea Schöllmann, said schools were encouraged to work with ākonga (students), their whānau and communities to ensure they were providing safe and inclusive school environments.