Girls are 19 per cent less active than boys their same age, a study of 550 students has found.
It also found that girls as young as eight were noticeably less physically fit than their male counterparts.
The study from the University of Canberra looked at the physical activity levels of the students from 29 primary schools in the ACT.
"Our findings suggest that school is a stronger influence on boys' activity levels compared to girls," researcher Rohan Telford said.
"On average, girls take almost 2,000 fewer steps a day than boys, and eight-year-old girls had 18 per cent lower cardio-respiratory fitness than boys of the same age.
"The data also showed that eye-hand coordination among girls was 44 per cent lower and there was a nine per cent lower perception of competence in physical education."
The research also showed that by age 12, boys received more support from their parents to be active.
The study looked at individual factors, such as fitness and body composition, family factors and environmental factors.
Mr Telford said the gap could be closed using a "multi-pronged approach" through family, school and extracurricular activities.
He also said the gap could be reduced by providing equal levels of encouragement and engagement for both genders.
But there needed to be more physical activity opportunities provided to girls.
The study was published in the journal PLOS ONE.