Background Stunting is still a major public health problem in low- and middle-income countries, including Indonesia. Previous studies have reported the complexities associated with understanding the determinants of stunting. This study aimed to examine the household-, subdistrict- and province-level determinants of stunting in Indonesia using a multilevel hierarchical mixed effects model. Methods We analyzed data for 8045 children taken from the 2007 and 2014 waves of the Indonesian Family and Life Surveys (IFLS). We included individual-, family-/household- and community-level variables in the analyses. A multilevel mixed effects model was employed to take into account the hierarchical structure of the data. Moreover, the model captured the effect of unobserved household-, subdistrict- and province-level characteristics on the probability of children being stunted. Results Our findings showed that the odds of childhood stunting vary significantly not only by individual child- and household-level characteristics but also by province- and subdistrict-level characteristics. Among the child-level covariates included in our model, dietary habits, neonatal weight, a history of infection, and sex significantly affected the risk of stunting. Household wealth status and parental education are significant household-level covariates associated with a higher risk of stunting. Finally, the risk of stunting is higher for children living in communities without access to water, sanitation and hygiene. Conclusions Stunting is associated with not only child-level characteristics but also family- and community-level characteristics. Hence, interventions to reduce stunting should also take into account family and community characteristics to achieve effective outcomes.