Aim: The mode of childbirth delivery can influence the child’s future health and the aim of this study was to explore the association between the delivery mode and the prevalence of early childhood caries. Methods: We searched the PubMed, Google Scholar and Cochrane databases up to September 15, 2020. Two independent reviewers screened the papers for relevance, extracted data and assessed the risk of bias with the Newcastle–Ottawa Scale. We performed a random effects meta-analysis to pool the prevalence of early childhood caries according to the mode of delivery. Results: The authors included 11 studies in the review, comprising 47,688 children with vaginal delivery and 10,994 with caesarean section (C-section). The publication years ranged from 1997 to 2020 and included birth cohorts, cross-sectional, register-based and case–control studies. We assessed three publications with low or moderate risk of bias. The median caries prevalence in the C-section group was 56.4% compared to 45.9% in the vaginal group and this difference was statistically significant (p < 0.05). The pooled overall odds ratio was 1.48 (95% CI 1.07–2.05) indicating a weak but statistically significant trend towards a higher caries occurrence among children delivered with C-section. The certainty of this finding was low due to heterogeneity and inconsistencies across the studies. Conclusion: We found a weak but inconsistent association between the mode of delivery and the prevalence of early childhood caries. Further studies based on representative, prospective cohorts reporting a standardized core outcome set are required to answer the research question with higher certainty.