Indonesia is ranked fifth among countries with the highest burden of stunting in children under five. This study aims to examine the determinants of stunting in children aged 0–2 years in Indonesia using data derived from the 2013 Indonesia Basic Health Survey. Twenty potential predictors of stunting, categorized into household and housing characteristics; maternal and paternal characteristics; antenatal care services and child characteristics were analyzed. Multilevel analyses were performed to examine the role of cluster/district/provincial differences, as well as individual/household level characteristics and stunting status. Of 24,657 children analyzed, 33.7% (95%CI: 32.8%–34.7%) were stunted. The odds of stunting increased significantly among children living in households with three or more children under five-years-old (aOR = 1.33, 95%CI: 1.03–1.72), households with five to seven household members (aOR =1.11; 95%CI: 1.03–1.20), children whose mothers during pregnancy attended less than four antenatal care services (aOR = 1.22, 95%CI: 1.08–1.39), boys (aOR = 1.33, 95%CI: 1.22–1.45), children aged 12–23 months (aOR = 1.89; 95%CI: 1.54–2.32), and children who weighed <2500 g at birth (aOR = 2.55; 95%CI: 2.05–3.15). The odds also increased significantly with the reduction of household wealth index. Integrated interventions to address environment, an individual level associated with stunting in Indonesia, from the environment- to individual-level factors are important.