"All people have the same rights and freedoms, regardless of their sexual orientation, gender identity and expression, and sex characteristics," the guidelines say.
"This means that schools need to:
• "Ensure inclusive environments for all young people.
• "Allow their ākonga [students] freedom of expression in relation to their gender identities and sexual orientation, including the right to determine their own identity and name.
• "Include content on the diversity of sex characteristics, sexuality, and gender identities in their curriculum programmes."
The new guidelines have been welcomed by Family Planning chief executive Jackie Edmonds as the first "meaningful change" since guidelines were first developed in 2002.
"It's close to 20 years since we first developed guidelines and we've had no meaningful change since then," she said.
"The Education Review Office and others working in this field know that implementation is patchy and not all young people are receiving the holistic relationship and sexuality education they deserve and as the ministry has prescribed."
The new version puts more emphasis on relationships, adopting the broader title of "relationships and sexuality education" to replace the term "sexuality education" used up to and including the last revision in 2015.
But the issue of teaching children about choosing their gender identity has been controversial. A Family First poll last year found that 54 per cent of New Zealanders did not believe that children should be taught that their gender can be changed through surgery and hormone treatment.
The new guidelines include separate documents for primary schools (Years 1 to 8) and secondary schools (Years 9 to 13).
Associate Education Minister Tracey Martin said the guideline "responds to feedback from the Korero Mātauranga [Education Conversation] calling on schools to take more action against bullying, violence and child abuse, for schools to be more inclusive, and for schools to help students recognise the importance of diversity and respect in relationships".
"They also respond to a recent Education Review Office (ERO) report noting that our curriculum would benefit from more information around sexuality issues such as consent, the use of digital technologies and relationships," she said.
"The revision takes into account the impact of social media, increasing awareness around sexuality and gender diversity, and the availability of more sexually explicit and confronting online content including pornography.
"Māori and Pacific views of sexuality and the importance of respecting cultural and family dynamics in relationships are strengthened, as is information about relationships and sexuality education for disabled learners."
The Ministry of Education will send hard copies of the new resource to schools next term and will provide online modules for teachers, showing examples of the new resource in practice.