A Western Cape pupil who was registered male at birth will start the new school term with a female identity.
His school took the unusual step of informing parents last month that the transgender pupil will wear a girl's uniform and be called by her female name.
The school had sought professional advice from a psychiatrist on the best way to support the pupil and her family.
Ron Addinall, a clinical social worker at the University of Cape Town, said he had assisted 12 transgender pupils at Western Cape schools with their social transition since last year.
These pupils are the lucky few.
In the absence of a policy from the department of basic education on how to manage transgender pupils, some principals have disregarded their plight.
Iranti, a media advocacy organisation that defends the rights of lesbians and transgender and intersex persons, said a transgender pupil in grade 7 at a Western Cape school became a laughing stock after the principal instructed a teacher not to register him as a boy as he was registered as a girl at birth.
"When you call somebody out by their birth name and not their chosen name, you are publicly shaming them," said Iranti's director, Jabu Pereira.
"Often teachers get uncomfortable and don't know what to do, so it becomes a joke."
Last year the Seshego Equality Court in Limpopo ordered the provincial education department to pay R60,000 in compensation to a transgender pupil who claimed her principal instructed other pupils to provoke her in the school's toilets.
Meanwhile, a teacher at the school that gave its blessings to the transgender pupil said one of the questions from the pupil was whether she would be allowed to use the girls' toilets.
"At the moment that's on hold until this whole thing is out in the community."
She said the pupil was "very excited and relieved that everything is now out in the open".
The school's principal said the reaction from parents had been very positive and supportive.
A Johannesburg mother whose 14-year-old enrolled in grade 8 at a school this year got the class teacher to delete the words "male" and "female" from the attendance register in a bid to prevent her child from being singled out as transgender.
Her child was born a girl but identifies as a boy.
"I want to see policy and practical guidelines in place immediately. I want principals to receive a directive saying, 'This is how you will behave.'"
The woman burst into tears as she told how her son had to wear very tight-fitting clothes and a binder to school to conceal his breasts. He will be undergoing breast-removal surgery in December.
She applied to the department of home affairs in June to have his gender and name changed.
"At school everybody thinks he's a boy."
Addinall said the youngest child he had assisted to socially transition was in grade 2.
"With prepubescent children, my role has been to meet with the family and the child and make the determination that he or she is definitely a transgender child. Parents have asked me to then assist in negotiating the social transition of the child at school.
"You now allow the child to start living the gender they articulate themselves to be."
He said because of the absence of a formal policy from the department, he had to negotiate with principals whenever he assisted a transgender pupil at a school.
Cape Town psychiatrist Dr Simon Pickstone-Taylor, who runs a gender identity development service at the Red Cross War Memorial Children's Hospital in the city, said studies showed that one in two transgender teenagers tried to commit suicide if they were not supported appropriately.
He said there were about 20 schools in Cape Town where pupils had socially transitioned.
He said he found principals and teachers to be generally very open and receptive.
"I bring up religion in the general talk because I think all prejudice boils down to either psychiatry or religion and it is important to dispel false beliefs. A lot of people equate homosexuality with being transgender."
Said Pickstone-Taylor: "Most of the kids don't want to be the 'transgender kid'; they just want to be a boy or a girl."
Western Cape education spokesperson Bronagh Hammond said the department was aware of a small number of cases in which pupils had asked to wear a different uniform, or be addressed by a different name. "These cases have been resolved in a manner which has embraced diversity and inclusivity within the school."
In 2015 a booklet called "Safer Schools for All: Challenging homophobic bullying in schools" was developed by the department of basic education.
It was developed in response to reports of bullying on the basis of gender and sexuality, reported by parents, pupils, schools and NGOs "requesting intervention that spoke to the knowledge gap existing in many schools on the rights of lesbian, gay, bisexual, transgender or intersex individuals."..