Purpose: To compare the effectiveness of the magnesium (Mg)-enriched formula vs. control formula in constipated infants. Methods: An open-label, interventional, and the comparator-controlled study was conducted to evaluate the effectiveness of the Mg-enriched formula in formula-fed infants ≤6 months old presenting with functional constipation according to modified Rome IV criteria. Infants were randomized 1:1 to intervention or control formula for 30 days. Parents recorded stool consistency (hard, normal, or watery) and frequency on days 1-7 and 23-29. Physicians recorded patient baseline characteristics and performed the clinical examination at the time of three patient visits (baseline, day 8, and 30). Results: Of the 286 recruited infants, 143 received the Mg-rich formula and 142 received the control formula. After 7 days, significantly more infants had stools with normal consistency with the Mg-rich formula compared to the infants fed with the control formula (81.8% vs. 41.1%; p < 0.001). The number of infants passing one or more stools per day was increased at day 7 in the Mg-rich formula group (86.7% vs. 68.2%; p < 0.001). At days 7 and 29, > 25% of infants responded completely to the Mg-rich formula compared to < 5% of infants fed with the control formula (p < 0.001). Parents of infants in the Mg-rich formula group were very satisfied with the treatment (80.8% vs. 10.2%), with the majority willing to continue treatment after 30 days (97.9% vs. 52.6%; p < 0.001). Conclusion: The Mg-rich formula significantly improved stool consistency and frequency compared to the control formula in constipated infants.