Socially transitioning refers to pupils asking to be addressed with different pronouns, or using different bathrooms.
The NHS said the training module had not been developed in line with the Department of Education (DoE).
It said: “Recently, there has been a rise in young people asking to make a social transition at school or college without the knowledge or involvement of their parents or carers.
“Supporting a social transition without the involvement of parents or carers can create complex difficulties within families and is not recommended. Secrets between parents or carers and their children are problematic and are likely to create further issues in the future.”
It added that when parents discover that changes have been made without their approval “this can increase risk and alienate parents and children".
Geoff Barton, the general secretary of the Association of School and College Leaders, said that the NHS and DoE guidance – when it is eventually published - needs to match.
He said: “It’s helpful that the NHS is providing guidance as this is obviously a source of information in which educators can have a high degree of confidence in navigating this complex and sensitive territory.”
“The frustration is that there continues to be a vacuum in terms of the official guidance that is supposed to be coming from the Department for Education.
The guidance also discourages teachers from allowing students to use different bathrooms without prior consent from parents
“This is such a highly charged subject that schools and colleges are likely to find themselves under fire whatever decision they make and they really do need to be able to point to the fact that they are following official guidance.
“At the moment — and for many years — this has not been the case, and the government has just left them hung out to dry.”
The NHS guidance is the first of its kind which refers to people questioning their gender identity.
It comes after a Policy Exchange report found that schools were regularly referring to pupils by different pronouns without their parents’ consent.