Objective: The objective was twofold: to assess the effect of physical activity (PA) interventions on children's and adolescents' cognition and metacognition; and to determine the characteristics of individuals and PA programs that enhance the development of cognitive and meta cognitive functions. Method: We systematically searched MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials, Web of Science, and PsycINFO databases from their inception to October 16, 2016. Intervention studies aimed at examining the exercise cognition interaction at a developmental age were included in this systematic review and meta-analysis. Random-effects models were used to calculate pooled effect size (ES) values and their corresponding 95% CIs. Subgroup analyses were conducted to examine the effect of participants' and PA programs' characteristics. Results: A total of 36 studies were included in this systematic review and meta-analysis. Pooled ES estimations were as follows: nonexecutive cognitive functions 0.23 (95% CI = 0.09-0.37); core executive functions 0.20 (95% CI = 0.10-0.30), including working memory (0.14 [95% CI = 0.00-0.27]), selective attention inhibition (0.26 [95% CI = 0.10-0.41]), and cognitive flexibility (0.11 [95% CI = 0.10 to 0.32]); and metacognition 0.23 (95% CI = 0.13-0.32), including higher-level executive functions (0.19 [95% CI = 0.06-0.31]) and cognitive life skills (0.30 [95% CI = 0.15-0.45]). Conclusion: PA benefits several domains of cognition and metacognition in youth. Curricular physical education interventions and programs aimed at increasing daily PA seem to be the most effective.