Perception is an essential component of children’s psychological development, which is foundational to children’s ability to understand and adapt to their external environment. Perception is also a crucial tool for understand and navigating one’s surroundings, enabling children to identify objects and react appropriately to settings or situations. Substantial evidence indicates that engaging in physical activity is beneficial for the development of children’s perceptual abilities, as the two are closely intertwined. Still, more research is necessary to gain a full understanding of the impact of physical activity on children’s perception. To further identify and quantify the effects of physical activity on a number of specific perceptions in children. Systematic review and meta-analysis. Searches were performed using five online databases (i.e., PubMed, SPORTDiscus, PsycINFO, Web of Science, and Cochrane Library) for articles published up to and including June 2023 to identify eligible citations. A total of 12 randomized controlled trials, encompassing 1,761 children under the age of 12, were analyzed. Overall, physical activity as an intervention showed a notable effect on the development of children’s perceptions. The meta-analysis indicated that participating in physical activity for 30 minutes around, daily, had a greater impact on children’s visual perception and executive functioning than on their motor perception, body perception, and global self-worth (SMD = 1.33, 95% CI: 0.75, 1.91, p < 0.001). The effects of physical activity on children’s perception performance varied by participant characteristics, with physical activity having better effects on body perception and overall self-worth in children who were obese or overweight. Furthermore, physical activity can also enhance executive function and attention in children with developmental coordination disorders. The effects of physical activity on children’s perception performance varied according to the intervention time, with different activity durations resulting in different perception performances. Therefore, parents and educators must prioritize an appropriate length of physical activity time for children to ensure their optimal growth and development. Registration and protocol CRD42023441119.