What are my rights if I’m refused permission by my school to wear uniform that affirms my gender identity?

There are no explicit rules stating that a school must allow you to wear a uniform that affirms your gender identity.  However, the Human Rights Commission has stated that transgender students should be able to wear a uniform that matches their gender identity (https://www.hrc.co.nz/files/3914/2378/4856/TGI-Fact-Sheet-A.html).  

The Ministry of Education has also suggested that schools may consider offering gender-neutral clothing choices when uniforms come up for review (http://health.tki.org.nz/Teaching-in-HPE/Policy-guidelines/Sexuality-education-a-guide-for-principals-boards-of-trustees-and-teachers).  This acts as advice to schools, rather than a legal requirement.