The associations among early childhood caries (ECC), socioeconomic status, and sugar consumption are of the utmost importance, due to their potential policy implications. The purpose of this study was to identify trends in ECC burden in children under 5 years old among European Union (EU) member states over time and to evaluate the relationship with its risk factors. Global Burden of Disease 2019 data were analyzed to estimate the burden of ECC over time, specifically incidence, prevalence, and years lived with disability (YLDs) for children under 5 years old. Four ecological variables with a potential effect on YLDs for ECC were used to investigate the association between 2014 and 2017. The YLDs rate was consistently higher among Eastern EU countries over time. Univariate models showed a positive significant association between at-risk-of-poverty rate and YLDs rate, while GDP per capita and urbanization were inversely associated with YLDs rate. In the multivariate analysis, sugar consumption, GDP per capita and urbanization showed significant association with YLDs rate. After stratification by region, association remained significant only in the Eastern EU countries between GDP, urbanization, and YLDs rate, while sugar consumption and at-risk-of-poverty rate had no significant impact on YLDs rates. This study found increasing ECC burden in the EU. The complexity of the problem indicates the need for innovative and personalized policy approaches to tackle the disease.