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Psychological stress and physical activity are interrelated, constituting a relevant association to human health, especially in children. However, the association’s nature remains elusive, i.e., why psychological stress predicts both decreased and increased physical activity. To test whether effects vary as a function of the level of analyses, we derived intensive longitudinal data via accelerometers and stress questionnaires from 74 children across 7 days as they went about their daily routines (\(\it n\) = 513 assessments). Multilevel modelling analyses revealed that between children, higher psychological stress predicted decreased physical activity (standardized beta coefficient = −0.14; \(\it p\) = 0.046). Concurrently, within those children, higher psychological stress predicted increased physical activity across days (standardized beta coefficient = 0.09; \(\it p\) = 0.015). Translated to practice, children who experienced more stress than others moved less, but children were more active on days when they experienced heightened stress. This suggests that the analyses level is crucial to the understanding of the association between psychological stress and physical activity and should be considered to receive unequivocal results. If replicated, e.g., including high-frequency sampling and experimental manipulation in everyday life for in-depth insights on underlying mechanisms and causality, our findings may be translated to individually tailored (digital) prevention and intervention strategies which target children's distress-feelings despite impairing their heightened physical activity in stressful situations and identify tipping points of chronic stress phases. Therefore, we especially call for more intensive longitudinal data approaches to tackle thus far neglected within-subject issues in the field of physical activity, sport and exercise research.