One aim of the Bunkeflo project is to evaluate if daily school physical activity (PA) is associated with higher final school grades and improved eligibility for upper secondary school. One elementary school extended PA throughout elementary school to 200 minutes/week while control schools continued with in mean 60 minutes/week. We then registered final school grades and eligibility for upper secondary school in children who began first grade in the intervention school during the years before the intervention (1994-1997) and in the children who started 1998-2003 (that is, who had daily PA during the 9 compulsory school years). We also registered final school grades and eligibility for upper secondary school in all Swedish children who started school 1998-2003. We found that boys in the intervention group had higher eligibility rates and higher grade scores than boys who finished the same school before the intervention was implemented as well as higher in all Swedish boys. These differences in were not seen in girls. Daily school PA through elementary school is associated with higher final grade scores and higher eligibility rates for upper secondary school in boys.