In boys, but not girls, a link between body composition and time spent exercising was observed.
The findings also suggest that measuring BMI alone does not accurately assess cardiovascular risk in children and that waist circumference and fitness measurements may give a clearer picture of the actual risk.
For the study, 84 boys and 140 girls, aged between seven and 10, were randomly selected from 12 schools.
Height, weight, waist circumference and BMI were determined for the children. BMI data was then used to assign the children to categories of normal weight, overweight and obese.
A validated running test was used to assess the level of cardiorespiratory fitness in the children.
Over the four-day study period, the boys spent more than an hour a day exercising vigorously, compared with just half an hour among girls.
Overall, all the children who scored well for cardiorespiratory fitness were found to be leaner and had smaller waists than those whose fitness was low.
But the amount of regular vigorous exercise only affected the boys’ weight.
Unlike girls, boys who performed the smallest amount of vigorous exercise were the fattest.
Lead researcher Juliette Hussey, head of physiotherapy at the University of Dublin, said: ‘We do not know why there is a different impact of exercise on body fat.’
It is difficult to say how much exercise children should be doing without conducting further research, said Ms Hussey.