Diocesan School for Girls in Auckland said the hijab was not allowed under their uniform code.
Responding to criticism, the $19,000-a-year school conceded that girls could wear hijabs only for a "Scarves in Solitarity" event on Friday in the wake of the terror attack targeting Muslims in mosques in Christchurch.
Diocesan School Principal, Heather McRae said in a statement: "Any girl or person who wants to show their respect for Muslim families affected in Christchurch by wearing a hijab to school on this day is most welcome to do so."
She explained that their uniform code is strict with girls prohibited from wearing jewellery or nail polish, long hair must be tied back and school blazers worn outside the grounds.
Ms McRea said: "Diocesan is a choice for an outstanding education by many parents.
"As a private girls' school, we celebrate diversity and inclusion.
"Our uniform policy is developed to help create a sense of oneness and family and is worn with pride by our students.
"All parents sign up to the Uniform policies when they join the school."
New Zealand's prime minister Jacinda Ardern was praised for wearing traditional Muslim clothing as she met survivors immediately after the attack.
A former student also told Newshub that she was not surprised the school had a strict dress code and during her time there she was unware of anyone wearing a hijab.
However, the school may be contravening human rights rules, which say discrimination on the grounds of religious belief is not allowed under both the Human Rights Act and the New Zealand Bill of Rights Act.
In a statement to the New Zealand Herald a school spokeswoman said: "The hijab has never been banned at Diocesan but that it is simply not part of the long standing school uniform code.
"There has never been a formal request from a family to have changes made to include it."