(1) Background: Stunting remains a challenge in Indonesia, where 30.8% of under-five children are stunted and may never reach full potential height and cognitive function. We aimed to investigate the risk factors of stunting in Nangapanda subdistrict, East Nusa Tenggara; (2) Methods: The design was cross-sectional study located in rural area as part of PINTERMIDI UI project. We collected quantitative data on social determinants, weight, height, hemoglobin, ferritin, serum zinc, CRP, worm infection, history of deworming, co-morbidity, food security, and nutrient intake; (3) Results: A total of 196 under-five children included and 74% households were food insecure. The prevalence of stunting was 29.9% in this population (31.8% worm infection, 30.3% iron deficiency, and 28.1% zinc deficiency). Multivariate analysis showed household with 5-8 members (AOR 3.076; 95% CI 1.132 – 8.356) and unsafe drinking water (AOR 1.702; 95% CI 0.825 – 3.512) were significant independent risk factors of stunting after adjusted by child’s gender, father’s occupation, caregiver’s education, monthly expenses, sanitary facilities, and food security status; (4) Conclusions: The number of household members is the only independent risk factor of stunting among children age 24-59 months in rural area of Eastern Indonesia. Development of nutrition sensitive intervention and promotion of family planning are needed in order to increase adequate child’s care and feeding practices in rural area of Eastern Indonesia.