Physical activity (PA) has been associated with enhanced cognition, brain development and concentration. This study evaluated whether increased physical education (PE) improved academic achievement. We recruited 304 children (55% boys) from a Swedish school in Skane County in 1998-2002 when they were six to seven years of age and followed them through all nine mandatory school years. Their PE level was increased from 60 to 200 minutes per week, and their results were compared with 73 885 control children (51% boys) in the county who graduated in the same years and did the standard 60 minutes of PE per week. Their academic achievements were measured as their final grade scores and the proportion of students eligible for upper secondary school. The eligibility for further education increased in the intervention boys by 6.8 percentage points and the mean grade score by 12.1 points, while in the control group as a whole, the eligibility rate decreased by 0.7 percentage points and the mean grade score increased by 1.7 points. No changes in eligibility rates or mean grade scores were seen in the intervention girls. Increasing weekly PE over nine years was associated with improved academic achievement in boys. ©2018 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.