In the past decades, interest in the relationship between physical activity and academic achievement has grown. Very few studies have been performed in school-aged children, and focus on cross-sectional designs has resulted in evidence for positive associations, but not for causal relationships. An important mediating role in the relationship between physical activity and academic achievement has been suggested for executive functions. The first aim of the present study is to examine causal effects of physical activity on (a) a wide range of executive functions in primary school children (e.g. working memory, inhibition, cognitive flexibility, and planning), and (b) multiple domains of academic achievement (mathematics, spelling, reading). The second aim is to study causal relationships between executive functions and academic achievement. The third aim is to examine effects of two school-based physical activity interventions in primary school children on executive functions, and academic achievement. A literature search including a meta-analysis on existing literature and available databases will be conducted. Results from the first part of the study (directing to the first two aims) will provide insight in optimal frequency, duration and intensity of physical activity and will be used for developing and implementing a cluster RCT on 24 primary schools (directing to the third aim). Participating schools will be randomly assigned to an aerobic intervention, a complex coordinative exercise intervention or control condition. The RCT will demonstrate effects of different types of interventions (aerobic exercises versus coordinative exercises) on academic achievement and a possible mediating role of executive functioning. Functional and structural neuroimaging will provide insight in underlying mechanisms on effects of physical exercise on the brain of school-aged children. Importantly, our RCT provides insight into feasibility of implementation in the Dutch primary school setting.