Early childhood caries (ECC) is a growing public health concern worldwide. Although numerous systematic reviews have been published regarding the association between breastfeeding and early childhood caries (ECC), the results remain inconclusive and equivocal. This systematic review synthesises the evidence on the association between breastfeeding and ECC. Five electronic databases and backward citation chasing were performed from inception until May 2023. A total of 31 studies (22 cohort studies and 9 case-control studies) were included in this review. The meta-analysis of the case-control studies showed statistically significant fewer dental caries in children who were breastfed for < 6 months compared to those who were breastfed for ≥6 months (OR = 0.53, 95% CI 0.41–0.67, p < 0.001). There was a statistically significant difference in dental caries between children who were breastfed for <12 months and those who were breastfed for ≥12 months (RR = 0.65, 95% CI 0.50–0.86, p < 0.002). Similarly, there was a statistically significant difference in dental caries in children who were breastfed for < 18 months compared to those who were breastfed for ≥18 months (RR = 0.41, 95% CI 0.18–0.92, p = 0.030). Nocturnal breastfeeding increases the risk of ECC compared with no nocturnal breastfeeding (RR = 2.35, 95% CI 1.42–3.89, p < 0.001). The findings suggest breastfeeding for more than 12 months and nocturnal breastfeeding increase the risk of ECC.