Background: Physical activity (PA) is considered one of the most important determinants of the health status in children, and predictor of morbidity/mortality in adults. The aim is to examine the relationship between physical fitness (PF), PA, obesity and academic performance (AP) in primary school children Methods: Cross-sectional studies including 91 primary school students, aged 9 to 12 years, from the province of Córdoba. Data was collected from April to June 2014. We measured PF using part of the EUROFIT fitness testing battery. The level of PA was measured as low or high PF and the level of obesity was measured using body mass index, waist circumference, percentage offal mass, lean body mass, percentage of lean mass and basal metabolism. AP by scores on the second quarter was based on the total average of scores of basic subjects and other subjects, including physical education. Cognitive performance was assessed by the Spanish overall and factorial intelligence test.Results: The results of AP were positively related to levels of PF. Students who achieve better PF score better in Maths, (P=0.019), Natural Sciences (P=0.024), Religion (P=0.018) and Physical Education (P<0.001). A direct association between maximal aerobic capacity with Mathematics (r=0.325, P=0.02), AP (r=0.349, P=0.001) and cognitive performance (CP)(r=0.312, P=0.003) was observed. There was also a direct association of better jump tests with higher AP (r=0.328, P=0.002).Conclusion: The AP is associated with higher levels of fitness. Therefore, the education system should consider implementing curriculum strategies favouring the improvement of the PF, and therefore the health and AP of students.