To investigate the effects of exercise on executive function in children, providing an evidence-based foundation to inform future research in school physical education and health education. Methods: We searched ten databases: Cochrane Library, Scopus, OVID, Web of Science, PubMed, EBSCOhost, SPORTDiscus, PsycINFO, CNKI, WANFANG DATA, VIP, and SinoMed, and eight articles were included. Applying the revised Cochrane Risk of Bias Tool for Randomized Trials (RoB2), funnel plots and Egger regression analysis were integrated with R meta-analysis to screen for publication bias. The quality of the evidence was appraised using the Grading system. Results: The included literature contained 2655 participants, with 1308 in the experimental group and 1347 in the control group. The results indicated that the aerobic exercise group considerably improved inhibitory control in children compared to the control group [SMD = 0.29, 95% CI (0.05, 0.54), P = 0.018]; working memory [SMD = 0.25, 95% CI (0.07, 0.42), P = 0.005]; and cognitive flexibility [SMD = 0.36, 95% CI (0.17, 0.54), P < 0.001]. However, the findings indicated that only aerobic exercise interventions extending beyond 50 weeks positively influenced academic performance in children [SMD = 1.19, 95% CI (0.34, 2.04), P = 0.006]. The results of an Egger regression analysis revealed that the p-values for inhibitory control, working memory, cognitive flexibility, and academic performance were more significant than 0.1. The Grade system said that the quality of evidence was all low regarding the level of evidence. Conclusion: Aerobic exercise enhanced executive function but only aerobic exercise interventions extending beyond 50 weeks demonstrated a significant effect on the academic performance of children. Due to the low quality of evidence presented in this study, additional high-quality randomized controlled trials are needed to confirm these findings.