The prevalence of stunting in lower and middle-income countries is relatively high especially in Indonesia which accounted for 27.5% of total children in 2019. In response to this, the government instituted stunting prevention program nationally, which includes supplementation of iron for high school female students and pregnant women, complementary feeding for young children, Integrated Health Service for children (Posyandu), and workshop and counseling of feeding practice for parents and health cadres. However, among many programs, evaluation on which programs succeed and what challenges are behind them rarely exists. The purpose of this study is to determine the factors associated with stunting and the effectiveness of the government-run stunting prevention program. The study used a qualitative approach with an in- depth interview method to explore the experience of health professionals in 10 Community Health Centers regarding the challenge of the stunting prevention program and the phenomenon of factors linked to stunting. Factors associated with stunting were low economic level, low education level, poor feeding practice, low birth weight, genetic disorder, infection, and poor sanitation. Challenges to the program included minimal effectiveness of supplementation of iron, invalid measurement, lack of monitoring and evaluation, and lack of sectoral collaboration. To prevent stunting, collaboration between various sectors and awareness and knowledge of stunting among parents and health cadres are needed.