Dietary patterns, exercise, sport, and physical activity have been shown to improve body composition in children. This systematic review with meta-analysis analyzed the effects of practicing football on body composition (fat mass, lean body mass, and bone mineral content) in children. An initial search in PubMed, Web of Science, and SPORTDiscus was carried out in April 2021 to identify relevant articles. Inclusion criteria required children up to 12 years of age with a minimum football intervention duration of 10 weeks. Methodological quality of the articles was evaluated using the PEDro scale. Between the 1803 articles originally founded, only 14 articles were included in the meta-analysis. A total of 1643 subjects between the 14 studies were identified. The review and meta-analysis were conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and used Review Manager and Full Meta-Analysis software. The results between the control and experimental groups showed significantly better lean body mass and fat mass values in the experimental group (p < 0.05). Football practice was positively associated with increases in lean body mass (mean difference of 1.55; 95% CI, 0.96, 2.15), decreases in fat mass (mean difference of -0.81; 95% CI, -1.49, -0.13), and increases in whole body bone mineral content (mean difference of 117.68; 95% CI, 83.69, 151.67). In conclusion, the results of this systematic review with meta-analysis suggest that football positively affects body composition in children. However, further research is needed to confirm the results for bone mineral content.