Stunting remains a major global malnutrition problem in children. A protocol for stunting prevention and management in Indonesia is needed to achieve the WHO's stunting reduction target by 40% in 2025. This study aimed to evaluate the effectiveness of a tiered referral system across different healthcare levels and the importance of animal proteins and food for special medical purposes (FSMP) in preventing and managing stunting in Indonesia. This one-group pre–post experimental study involved children under 5 years old from 14 regencies in Indonesia. All subjects initially received education about breastfeeding and animal proteins. Eligible subjects were then given daily animal protein (milk and/or egg) supplementation. Subjects with weight faltering, underweight, or wasting were referred and given nutritional intervention for 2 weeks. If treatments failed to normalize undernutrition, subjects were referred to regional hospitals. Those confirmed as stunted or with low birth weight were directly referred for treatment and FSMP as indicated. A total of 1841 subjects received egg and/or milk supplementation. In 6 months, animal protein supplementation prevented weight faltering in 1320/1841 subjects (71.7%; 95% CI 69.6%–73.8%). Red flags management successfully prevented stunting in 536/709 subjects (75.6%; 95% CI 72.4%–78.8%) in 2 weeks. FSMP prescription for catch-up growth in regional hospitals led to stunting recovery in 166/381 subjects (43.6%; 95% CI 38.6%–48.5%) in ±14 weeks. A tiered referral system with well-defined treatment guidelines is crucial to address stunting in Indonesia. Timely referral and FSMP prescription for catch-up growth can effectively treat stunting. Animal proteins and education are keys to preventing stunting in children. © 2025 The Author(s). Food Science & Nutrition published by Wiley Periodicals LLC.