It has been suggested that small intestinal bacterial overgrowth (SIBO) could cause nonalcoholic fatty liver disease (NAFLD), but this association was not examined in children by meta-analysis. This meta-analysis aimed to determine the association between SIBO and NAFLD in children. The electronic databases PubMed, Embase, and Cochrane Library were searched for studies published before April 22, 2021. The outcome was the association between SIBO and NAFLD. Three studies and 205 children were included. All three studies reported the association between SIBO and NAFLD. Children with SIBO were more likely to have NAFLD (odds ratio = 5.27, 95% confidence interval (CI): 1.66–16.68, P<0.001; I2 = 63.5%, Pheterogeneity = 0.065). When directly pooling the reported relative risks (RR) from two studies, children with NAFLD had an over 2-fold increased relative risk of developing SIBO (RR = 2.17, 05%CI: 1.66–2.82, P<0.001; I2 = 0.0%, Pheterogeneity = 0.837). This meta-analysis reports a possible association between SIBO and NAFLD in children.