Background and Objectives: Cognitive performance is essential for children, given this is a critical stage of brain growth and development. This systematic review and meta-analysis aimed to ascertain if physical activity or micronutrients impact cognitive performance in children. Materials and Methods: Electronic databases (PubMed and Scopus(R)) were searched for relevant articles published between 2012 and 2021. We emphasized randomized controlled trials (RCTs) that examined the effect of physical activity and micronutrients on cognitive performance. Data from eligible studies were gathered and evaluated using random-, fixed- or pooled-effects models with 95% confidence intervals (95% CI). Results: Physical activity appeared to improve both Mathematics (d = 1.12, 95% CI: 0.56, 1.67) and attention (d = 0.65, 95% CI: 0.15, 1.14) performances. The micronutrient vitamin B12 had a positive effect on Mathematics (d = 2.39, 95% CI: 0.79, 3.98), English (d = 5.29, 95% CI: 2.76, 7.83), Geography (d = 5.29, 95% CI: 2.76, 7.83), Science (d = 3.39, 95% CI: 2.62, 4.16) and Arts (d = 3.32, 95% CI: 1.84, 4.79). Zinc was found to positively affect English (d = 3.78, 95% CI: 0.44, 7.13), Geography (d = 4.77, 95% CI: 0.56, 8.98) and Arts (d = 2.39, CI: 0.33, 4.45). Iron positively affected Mathematics (d = 1.29, 95% CI: 0.54, 2.06), English (d = 1.29, 95% CI: 0.44, 7.13), Geography (d = 4.77, 95% CI: 0.56, 8.98) and Arts (d = 2.39, 95% CI: 0.33, 4.45). Conclusions: A more comprehensive intervention with a specific dose/level of physical activity, an increased range of cognitive performance, and a well-designed study design that accounts for dietary intake and other health outcomes are required for future studies.