To assess the relationship between fat mass percentage (FMP) and glucose metabolism in children aged 0−18 years we performed a systematic review of the literature on Medline/PubMed, SinoMed, Embase and Cochrane Library using the PRISMA 2020 guidelines up to 12 October 2021 for observational studies that assessed the relationship of FMP and glucose metabolism. Twenty studies with 18,576 individuals were included in the meta-analysis. The results showed that FMP was significantly associated with fasting plasma glucose (FPG) (r = 0.08, 95% confidence interval (CI): 0.04−0.13, p < 0.001), fasting plasma insulin (INS) (r = 0.48, 95% CI: 0.37−0.57, p < 0.001), and homeostasis model assessment (HOMA)- insulin resistance (IR) (r = 0.44, 95% CI: 0.33−0.53, p < 0.001). The subgroup analysis according to country or overweight and obesity indicated that these associations remained significant between FMP and INS or HOMA-IR. Our results demonstrated that there is a positive relationship between FMP and FPG. Moreover, subgroup analysis according to country or overweight and obesity indicated that FMP is significantly associated with INS and HOMA-IR. This is the first known systematic review and meta-analysis to determine the associations of FMP with glucose metabolism in children and adolescents.