Background: Early Childhood Caries (ECC) is a common dental condition in children under six years, with Streptococcus mutans playing a key role in its development. The balance between demineralization and remineralization is essential for maintaining tooth integrity. Casein Phosphopeptide-Amorphous Calcium Phosphate (CPP-ACP) has anti-cariogenic properties and promotes remineralization. This study compares the effectiveness of CPP-ACP application versus Glass Ionomer Cement (GIC) restorations in reducing S. mutans in children with ECC.Materials and Methods: Eighty children were enrolled, with baseline S. mutans colony-forming units (CFU) assessed through stimulated saliva samples. Participants were randomly assigned to two groups: Group A received CPP-ACP application, and Group B underwent GIC restoration. Follow-up saliva samples were collected at 1 week, 1 month, and 3 months to reassess CFU counts. Results: No significant baseline difference in CFU counts was found between the groups (P = 0.7344). Post-treatment, the case group exhibited a significant reduction in CFU counts compared to the control group (P = 0.0002). Gender-based analysis revealed significantly lower CFU counts in both male and female participants in the case group at all time points (P < 0.05). These findings demonstrate the sustained efficacy of CPP-ACP with GIC restorations in reducing S. mutans. Conclusion: CPP-ACP application effectively reduces S. mutans levels in children with ECC, highlighting its potential as an adjunct to GIC restorations. Further studies with longer observation periods are needed to confirm these results.