Dr Mary Bousted said boys find it easier to challenge classes and are less likely to be picked up on this behaviour than girls.
She added that it could be "dangerous" for young women to speak up in the classroom as it could make them the target of abuse by their peers.
Dr Bousted, general secretary of the Association of Teachers and Lecturers said: "Teachers, understandably, don't like disruption from anyone, but it is the boys who find it easier to challenge and dominate lessons.
"Meanwhile, it can be dangerous for girls to be assertive, speak confidently, take up class talk time or defend their opinions."
The comments come just weeks after another school leader said schools should encourage girls to be disruptive to help them become successful later in life.
Dr Kevin Stannard, director of innovation and learning at the Girl's Day School Trust, said "disruptiveness" can be empowering and teach young women skills they will need to gain university places and perform well in the workplace.