The report, by the Joseph Rowntree Foundation, also found that girls cope with problems differently to boys.
Instead of facing difficulties like bullying they just stay away from school or become withdrawn. There are also differences in the way girls and boys bully, with girls using gossip instead of violence.
The researchers - who interviewed 81 girls in six areas of England - say most girls want more support from schools, their own spaces away from boys and more counsellors.
They also discovered white girls think teachers are stricter with black girls. Official statistics say black girls are four times more likely to be excluded, but the researchers found the white girls they talked to didn't realise this.