Background The purpose of this paper is to review relationships of academic performance and some of its determinants to participation in school-based physical activities, including physical education (PE), free school physical activity (PA) and school sports. Methods Linkages between academic achievement and involvement in PE, school PA and sport programmes have been examined, based on a systematic review of currently available literature, including a comprehensive search of MEDLINE (1966 to 2007), PSYCHINFO (1974 to 2007), SCHOLAR.GOOGLE.COM, and ERIC databases. Results Quasi-experimental data indicate that allocating up to an additional hour per day of curricular time to PA programmes does not affect the academic performance of primary school students negatively, even though the time allocated to other subjects usually shows a corresponding reduction. An additional curricular emphasis on PE may result in small absolute gains in grade point average (GPA), and such findings strongly suggest a relative increase in performance per unit of academic teaching time. Further, the overwhelmingly majority of such programmes have demonstrated an improvement in some measures of physical fitness (PF). Cross-sectional observations show a positive association between academic performance and PA, but PF does not seem to show such an association. PA has positive influences on concentration, memory and classroom behaviour. Data from quasi-experimental studies find support in mechanistic experiments on cognitive function, pointing to a positive relationship between PA and intellectual performance. Conclusion Given competent providers, PA can be added to the school curriculum by taking time from other subjects without risk of hindering student academic achievement. On the other hand, adding time to "academic" or "curricular" subjects by taking time from physical education programmes does not enhance grades in these subjects and may be detrimental to health.