The guidance, published by the Scottish Government on Thursday, covers a range of issues, including the use of bathrooms, residential trips, and how teachers should deal with the situation of a pupil saying they are transgender.
It also has an additional focus on ensuring any policy takes into account the impact on all students, with a particular focus on the impact on girls in schools.
The 70-page document is non-statutory and states that it aims to “help school staff … provide transgender young people with the best possible educational experiences”.
It has been widely backed by charities such as LGBT Scotland and Scotland’s Children and Young Person’s Commissioner.
Announcing the guidance, education secretary Shirley-Anne Somerville said transgender pupils faced “many issues” and the guidance would provide schools with “practical suggestions”.
She said: “Pupils are happier and learn more at school when they feel safe, respected and included.
“We know transgender young people can face many issues in schools and that teachers and staff must have the confidence and skills to support their mental, physical and emotional health.
“This guidance outlines how schools can support transgender young people while ensuring that the rights of all pupils are fully respected. It provides schools with practical suggestions. The guidance is not prescriptive and does not promote transitioning.”
Scotland’s largest teaching union, the EIS, also backed the guidance, but called for “sufficient time” for the document to be considered alongside other requirements for teachers.
A spokesperson said: “Schools should be places where all young people feel safe, included and supported, including those who are transgender. Providing guidance to school staff on supporting young people who are trans is a potentially helpful contribution to schools understanding and meeting the specific needs of this group.
"What is also needed, though, is sufficient time for teachers and other school staff to engage with the guidance and to consider its relationship to wider equality considerations, through good quality professional learning and collaboration.”
Bruce Crawford, Scotland’s children’s commissioner, said: “We are pleased that the Scottish Government has heeded calls, including from my office, to produce new guidance to help schools support transgender young people.”
LGBT charities also backed its publication, with Dr Mhairi Crawford, chief executive of LGBT Youth Scotland, saying the guidance should help improve the lives of young trans people.
She said: “We welcome the publication of the Scottish Government’s resource on supporting trans young people in schools and hope that all teachers take the opportunity to put its guidance into practice in their classrooms, allowing all learners to achieve their full potential.
“Our research shows that school is the area where trans young people experience the most discrimination and this must be addressed.”
Vic Valentine, manager of Scottish Trans Alliance, said: “When I talk to trans young people today, I’m often really encouraged when I hear just how much more they feel able to be themselves at school than I felt able to be.
"But even though things are getting better, far too many trans young people continue to have bad experiences at school.
“That’s why we strongly welcome this Scottish Government guidance, that will give schools and teachers the tools they need.”