This study examined factors associated with stunting in children aged <2 years in eastern Indonesia. Data were derived from three national cross-sectional surveys of Indonesia. The outcome variable was stunting (low length-for-age) in children aged <2 years. Nineteen potential predictors from community- to individual-level characteristics were identified. Multilevel analyses were performed, adjusting for cluster sampling with random effects for cluster and strata. We used data from the 2010, 2013, and 2018 Indonesian Basic Health Research. Information from 6,076 children aged <2 years from Nusa Tenggara Barat, Nusa Tenggara Timur, Sulawesi, Maluku, and Papua regions were used. We found that the proportion of stunted children aged <2 years in eastern Indonesia decreased between 2010 and 2018. Significant predictors of stunting included living in West Nusa Tenggara (adjusted odds ratio (aOR)=1.09; 95% confidence interval (CI): 1.02–1.16), and East Nusa Tenggara region (aOR=1.36; 95%CI: 1.28–1.45), belonging to a household with <3 children under-five (aOR=1.32; 95%CI: 1.13–1.56), being from a poor household (aOR=1.20; 95%CI: 1.08–1.33) and born to less educated mother (aOR=1.27; 95%CI: 1.03–1.58). Furthermore, stunting were more likely among males (aOR=1.29, 95%CI: 1.19–1.40), those aged 12–23 months (aOR=2.01; 95%CI: 1.65–2.44), with low birth weight (aOR=1.91; 95%CI: 1.41–2.61), and with gestational age of <37 weeks at birth (aOR=1.14; 95%CI: 1.05–1.23). Multiple factors contribute to stunting in eastern Indonesia, highlighting the need for comprehensive and targeted initiatives. Poverty reduction, healthcare system improvement, family planning, and continued health promotion strategies are necessary to reduce stunting prevalence.