The government of Serdang Bedagai Regency initiated a supplementation program to reduce the high prevalence of stunting in the area by delivering extra supplementation, which were nutritious biscuits from national government and fish-based supplement produced from local resources. A 6-month study from April 2022 to September 2022 was conducted to monitor and evaluate the government program that involved 219 under-5-year-old children with height-for-age Z-score (HAZ-score) below − 2. We observed the stunting prevalence reduction by 37.00%, where 81 children recovered from stunting (HAZ-score ≥ − 2). Furthermore, the mean HAZ-score and WHZ-score (Weight-for-Height Z-score) were monitored to significantly improve by 0.97 ± 1.45 (P-value = 1.74e−14) and 1.00 ± 2.18 (P-value = and 2.40e−8), subsequently. The most significant improvement in HAZ-score was monitored among children receiving fish-based supplements with 1.04 ± 1.44 improvement (P-value = 6.59e−17). Then, a significant WHZ-score improvement was reported from children consuming fish-based supplements and a combination of fish-based supplements with nutritious biscuits (P-value = 2.32e−8 and 5.48e−5) by 1.04 ± 2.29 and 0.83 ± 1.84, respectively. The results of the observation become evidence that the program could effectively reduce the prevalence of stunting in children below five years old, especially among children who received locally produced fish-based supplements.