This cross-sectional study in four stunting locus villages in East Nusa Tenggara, Indonesia (the province with the highest stunting prevalence in the country) found a stunting prevalence of 22.3% among children aged 24–59 months. Lack of maternal knowledge (AOR: 5.310) and negative parenting (AOR: 3.026) were the strongest risk factors for stunting. The findings highlight the need for targeted health education and parenting interventions in these high-priority villages to meet Indonesia's 2024 stunting reduction target of 14%.