Dental caries remains a prevalent global health concern, necessitating effective non-invasive management strategies. This study compares the efficacy of fluoride varnish and resin infiltration in arresting early enamel caries lesions. A randomized controlled trial was conducted on 120 participants aged 6–12 years with non cavitated enamel lesions. Subjects were randomly assigned into two groups: fluoride varnish application (Group A) and resin infiltration (Group B). Caries progression was assessed at baseline, three months, and six months using ICDAS-II scoring and quantitative light-induced fluorescence (QLF) analysis. The results indicated a statistically significant reduction in lesion progression in both groups (p < 0.05), with resin infiltration demonstrating superior lesion stability compared to fluoride varnish at the six-month follow-up (p = 0.01). The findings suggest that while both interventions effectively manage early carious lesions, resin infiltration offers enhanced remineralization and lesion masking, making it a promising alternative to traditional fluoride therapy. Further longitudinal studies are recommended to evaluate long-term outcomes.