The aim of this paper is to systematically review the literature to determine whether early childhood caries (ECC) is significantly associated with caries development in permanent teeth among school children and adolescents, and to identify the association of other risk factors over 24 months. A systematic literature search was performed in four electronic databases and via a manual search from inception to 28 July 2022. Independent study selection and screening, data extraction, evaluation of risk of bias using ROBINS-I tool and certainty of evidence with GRADE were performed. Ten cohort studies were included, all of which identified that ECC significantly increased the risk of caries in permanent teeth. Meta-analysis suggested children with ECC were three times more likely to develop caries in their permanent teeth (OR, 3.22; 95% CI 2.80, 3.71; p < 0.001), especially when the lesions were in primary molars and progressed to dentine. However, the certainty of evidence was substantially compromised by serious risk of bias and inconsistency between studies. There were inconsistent findings between socioeconomic or behavioural factors on caries development, which could not be pooled for meta-analyses. ECC significantly increases the likelihood of caries development in permanent teeth. Evidence on the association of socioeconomic and oral health behavioural factors is weak.