Introduction: Various trial and epidemiological studies consistently documented the association between maternal folic acid supplementations and neural tube defects. However, existing literatures revealed inconclusive findings about maternal periconceptional folic acid supplementations and the risk of congenital heart defects. Thus, the current systematic review and meta-analysis was aimed to estimate the pooled association between maternal periconceptional folic acid supplementations and congenital heart defects. Methods: Electronic searches of PubMed, Web of Science/Scopus, Cochrane library and Google Scholar databases were conducted to access the required studies published up to March 2021. Predetermined eligibility criteria were used for study selections. Data extraction were independently done on excel. STATA version 14 software was used to calculate the pooled effect size with 95% confidence intervals (95% CI) of maternal periconceptional folic acid supplementations on congenital heart defects using the DerSimonian and Laird random effects meta-analysis (random effects model). Statistical heterogeneity was checked using the Cochran Q test (chi-squared statistic), I2 statistic, and by visual inspection of the funnel plot. Results: A total of 37 studies of case–control, cohort and randomized controlled trial in nature were included in the review. The finding of the present systematic review and meta-analysis indicated that periconceptional folic acid supplementation significantly decreases the risk of congenital heart defects (risk ratio (RR), 0.79; CI, 0.71, 0.89). Both Cochrane Q test statistic (χ2 = 19.33, p = 0.962) and I2 test statistic (I2 = 0.0%, p = 0.962) did not reveal statistically significant heterogeneity among included studies. In this meta-analysis, traditional funnel plot, Begg’s funnel plot, Egger’s weighted regression (p = 0.13) as well as Begg’s rank correlation statistic (p = 0.676) revealed no evidence of publication bias. Conclusion: The present systematic review and meta-analysis found that maternal periconception folic acid supplementation was significantly associated with the risk of congenital heart defects. The risk of congenital heart defects was significantly reduced by 21% among those children of mothers who use periconceptional folic acid supplementations in high-income countries. We recommend that a large prospective study be conducted to investigate the association between maternal periconceptional folic acid supplementation and occurrence of congenital heart defect of various types, especially in the developing countries.