Aim: Aim of the current study was to assess the anticariogenic effectiveness of different fluoride varnishes on artificially induced enamel lesions employing scanning electron microscope. Materials and methods: Eighty healthy, normal premolars without dental caries that were extracted in course of orthodontic therapy with all the surfaces intact were included in this study. A window, 4 × 4 mm, was made discernible on the buccal surface of each sample tooth. A demineralizing solution at 37°C was used to immerse the teeth for 48 hours to induce artificial lesions on the surface of the enamel. Following preparation of the artificial enamel lesions, the 80 premolar teeth were allocated into the four groups (20 each) depending on the fluoride varnish system used as Group I: control, Group II: Duraphat varnish, Group III: MI Varnish, and Group IV: Clinpro White Varnish. The anticariogenic effectiveness of different fluoride varnishes was evaluated employing a scanning electron microscope (SEM). Results: The MI Varnish (fluoride varnish) group exhibited slightly greater (127.20 ± 0.14) mean demineralized lesions, pursued by Clinpro White Varnish use (126.88 ± 0.09), the control group (126.36 ± 0.10) and the Duraphat varnish (124.14 ± 0.08) in that order. Greater mean areas of remineralization were found with use of MI Varnish (92.40 ± 0.09), pursued by the Duraphat varnish use (106.68 ± 0.12), use of Clinpro White Varnish (112.36 ± 0.08), and then the control group (123.08 ± 0.18) in that order. Statistically significant differences were noted between the experimental groups employing the various fluoride varnishes (p <0.001). Conclusion: The current research concluded that the MI Varnish group presented a superior protective potential in comparison with Duraphat varnish and Clinpro White Varnish groups. Clinical significance: Mineral exchanges among teeth and saliva render incipient enamel lesions reversible. A 5% sodium fluoride varnish is the MI Varnish that is composed of casein phosphopeptide–amorphous calcium phosphate (CPP-ACP) to provide an excellent fluoride varnish that makes available additional bioavailable fluoride, calcium, and phosphate. Therefore, it may be fruitfully utilized in remineralization of initial carious lesions. CPP-ACP may be employed in clinical practice for drawing back or ceasing initial carious lesions.