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The current study focused on the effects of an 8-week motor skill-based physical activity (i.e., gymnastics) program on the contingent negative variation derived from event-related brain potentials (CNV-ERP) during a working memory task in children. Children aged 7–10 years old were assigned to a gymnastics group (n = 26) or a wait-list control group (n = 24). The gymnastics group engaged in a gymnastics program whereas children in the control group were asked to maintain their typical routine during the intervention period. Working memory performance was measured by a delayed-matching working memory task, accompanied by CNV-ERP collection. The results revealed significant improvement of response accuracy from pre-test to post-test in the gymnastic group regardless of memory demands. Moreover, significant increase from pre-test to post-test in the initial CNV was observed in the gymnastic group regardless of memory demands. Bivariate correlations further indicated that, in the gymnastic group, increases in response accuracy from pre-test to post-test were correlated with increases in initial CNV from pre-test to post-test in task conditions with lower and higher memory loads. Overall, the current findings suggest that up-regulation of proactive control may characterize the beneficial effects of childhood motor skill-based physical activity on working memory.