This systematic review synthesized current literature regarding the effect of physical activity (PA) interventions on brain structure (BS) and brain function (BF) in healthy children. This review followed the Preferred Reporting Items for Systematic Reviews protocols and used the Rayyan web for data extraction. Eleven experimental studies were included. Specifically, six studies conducted chronic PA interventions, and the others applied acute PA interventions. Evidence from five articles (45.45%) confirmed that PA interventions had beneficial effects on brain structure and function in healthy children, including enhancing brain activation and microstructural plasticity. These articles shared a study protocol and were conducted in school settings, indicating homogeneity. Due to the technical complexity and limitations involved, there are few studies on brain health and development. Future research is necessary to validate and evaluate the effectiveness of PA interventions on brain structure and function in healthy children.