Background: Congenital heart diseases are among the most common birth defects, significantly impacting infant health. Recent evidence suggests that exposure to endocrine-disrupting chemicals may contribute to the incidence of congenital heart diseases. This study systematically reviews and analyzes the association between maternal endocrine-disrupting chemicals exposure and congenital heart diseases. Methodology: This systematic review and meta-analysis followed the Cochrane Handbook and PRISMA guidelines. We included studies assessing the link between maternal exposure to various endocrine-disrupting chemicals and the incidence of congenital heart diseases without restricting the study design or exposure assessment methods. Data were extracted from four databases, including PubMed, Scopus, Web of Science, and Cochrane Library, up to June 2024. Quality assessment of observational studies was conducted using the Newcastle–Ottawa Scale. Statistical analysis was performed using RevMan software version 5.3, presenting results as odds ratios with 95% confidence intervals. Results: Fifty-nine studies were included in the meta-analysis. The pooled analysis revealed a significant association between maternal endocrine-disrupting chemical exposure and the incidence of congenital heart diseases when measured using human samples (odds ratio = 1.63, 95% confidence interval [1.35–1.97], p < 0.00001). Notably, exposure to heavy metals, polycyclic aromatic hydrocarbons, and perfluoroalkyl compounds was strongly associated with congenital heart diseases. However, non-sample-based methods showed no significant overall correlation (odds ratio = 1.08, 95% confidence interval [0.93–1.26], p = 0.30), except for housing renovation compounds, which were linked to a higher incidence of congenital heart diseases. Conclusions: Maternal exposure to specific endocrine-disrupting chemicals, particularly heavy metals and polycyclic aromatic hydrocarbons, significantly increases the risk of congenital heart diseases. These findings underscore the need for preventive measures to reduce endocrine-disrupting chemicals exposure during pregnancy and further research to elucidate the underlying mechanisms.