The group has reported that students have said that they are not confident in reporting the abuse they have been receiving, and that that strong leadership from school leaders and local authorities is needed to tackle the issue.
This news comes in conjunction with a new anti-bullying strategy released by the Scottish government developed with the help of LGBT+ organisations.
LGBT Youth Scotland has said that its study shows that transgender youth face more difficulty than their LGB peers, facing greater levels of bullying.
Megan McIntyre, a member of LGBT Youth Scotland's national youth council, said homophobic bullying is often not taken seriously when reported.
'I had to move school because they wouldn't deal with the bullying at all.' She told the BBC. 'Once I had moved my new school wasn't much better. As a result, my attendance dropped as I didn't want to be there. I wasn't in a good place.'
A spokesperson for the Scottish government has spoken out against anti-LGBT+ bullying, saying 'Respect for All, the refreshed national anti-bullying strategy for children and young people, which has been developed in collaboration with organisations including LGBT Youth Scotland and Stonewall Scotland, will take a holistic approach to tackling the issue.
'Last week, Deputy First Minister John Swinney wrote to the Scottish Parliaments Equalities and Human Rights Committee to welcome their input into the process and agree to put the publication on hold to allow for meaningful engagement.
'We have also committed to a programme of teacher education on equality for all, proving further funding where necessary and have updated relationship teaching guidance.'