LGBT Youth Scotland said its research suggested more needed to be done to ensure LGBT young people felt safe.
It urged those affected to understand their rights and report discrimination.
The charity said not every young person was aware of what constituted a criminal act under hate crime legislation .
In an online survey of LGBT people aged 13 to 25 conducted by the charity, 49% of the 273 respondents said they felt safe and supported by the legal system. The figure fell to 40% among those who identified as transgender.
Half of those surveyed said they were aware of their rights, while a similar proportion (53%) said they would feel confident in reporting a crime they experienced to the police.
Among transgender young people the figure dropped to 48%, while bisexual women were the least likely to feel confident reporting a hate crime at 46%.
Just over half (51%) of transgender young people said they felt safe using public transport.
While the charity has welcomed an increase in the reporting of hate crimes, YGBT Youth Scotland has recommended that campaigns, activities and lesson plans be developed for use in schools, with specific reference to hate crime.
Chief executive Fergus McMillan said: "In Scotland, we are fortunate to have strong hate crime legislation that is inclusive of transgender identities yet the safety report shows a gap in knowledge and confidence for transgender young people in particular.
"When young people know about their rights, and have confidence in the process, they are more likely to be willing to report.
"An increase in reported crimes since the introduction of the legislation is certainly positive, yet more must be done to ensure that LGBT young people feel safe in their communities, understand their rights and how to report discrimination and harassment, and have the confidence to report."
Many lesbian, gay, bisexual and transsexual (LGBT) young people still encounter harassment in public spaces, according to a Scottish charity.