Abstract Background Asthma is the most common respiratory disease among children, while atopic diseases such as atopic dermatitis affect about 20% of infants under 2 years of age. Studies suggested that these conditions might be related to prenatal depression or anxiety. This study aimed to explore the association between prenatal mental disorders and childhood asthma or atopic disease in a systematic review and meta-analysis. Methods PubMed, Embase, and the Cochrane Library were searched up to May 2020. The primary outcome was childhood asthma and childhood atopic dermatitis. Random-effects models were used because of high heterogeneity indicated by I2 > 50% and Q-test P < 0.10. Results A total of 598 studies were initially identified, but nine studies met the inclusion criteria. Prenatal mental disorder was associated with childhood asthma (n = 6 studies; ES = 1.146, 95%CI: 1.054–1.245, P = 0.001; I2 = 93.5%, Pheterogeneity < 0.001) whereas no significant association was found for childhood atopic dermatitis (n = 4 studies; ES = 1.211, 95%CI: 0.982–1.494, P = 0.073; I2 = 78.5%, Pheterogeneity < 0.001). Childhood asthma seems to be related more to depression (n = 1 study; ES = 1.170, 95%CI: 1.061–1.291, P = 0.002) and anxiety/depression (n = 4 studies; ES = 1.157, 95%CI: 1.050–1.275, P = 0.073; I2 = 95.3%, Pheterogeneity < 0.001). Conclusion This meta-analysis demonstrated that prenatal mental disorders increase the risk of childhood asthma. We limited the included samples to pregnant women to investigate the association between prenatal psychological factors and offspring’s physical health. Future studies should include large high-quality cohort studies to investigate the behavioral, environmental, and genetic causes for this association.