The guidance, which is non-statutory, is designed to help education authorities, grant-aided and independent schools, to make decisions effectively.
It cannot be prescriptive about what is required in individual circumstances, the Government has said.
It contains real-life examples, best practice and advice on a wide range of issues known to affect transgender pupils including bullying, safety and privacy.
The Government said that it also recognises the importance of privacy and safe spaces for girls and boys within schools.
“Pupils are happier and learn more at school when they feel safe, respected and included.”
Shirley-Anne Somerville, education secretary
Education secretary Shirley-Anne Somerville, right, explained the guidance outlines how schools can support transgender young people.
“Pupils are happier and learn more at school when they feel safe, respected and included,” she said.
“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.”
Carrie Lindsay, president of the Association of Directors of Education Scotland, said: “ADES welcomes any resource that helps give schools information and advice about how they can ensure an inclusive school ethos and environment for all of our children and young people.”
The guidance was welcomed by the charity, Time for Inclusive Education (TIE).
They said: Transgender young people can often experience a range of issues at school which impact on attainment and wellbeing, including prejudice-based bullying.
“It’s important that schools and teachers know how to provide support. We welcome this new guidance.”
Meanwhile, Fans going to the TRNSMT festival in September will have to show proof of a negative Covid test before being allowed in, organisers have said.
The music event is running from 10-12 September at Glasgow Green, after moving from its traditional July slot.
The entry policy was decided following discussions with the Scottish government and Glasgow City Council.
Those attending over multiple days will be required to take a second lateral flow test 48 hours after the first.
The policy will also apply to the Biffy Clyro concert at Glasgow Green on 9 September.
Top picture: First Minister Nicola Sturgeon campaigning with young people for transgender rights.