This study aimed to determine the effects of three different varnish materials (containing casein phosphopeptide-amorphous calcium phosphate, nano-hydroxyapatite, and fluoride) on enamel. Thirty-three extracted human third molars were used for specimen preparation. These were demineralized using phosphoric acid. Three experimental groups (n = 11) were treated with 3M™ Clinpro™ White Varnish, MI Varnish®, and Megasonex® toothpaste, respectively, every twenty-four hours for fourteen days. Analysis of the microhardness of the specimens’ enamel surfaces was carried out via the Vickers method, and by scanning electron microscopy/energy dispersive X-ray spectroscopy (SEM/EDS). Analysis was performed at three stages: at baseline value, after demineralization, and after the period of remineralization. Data were subjected to Scheffe’s post hoc test. The mean microhardness values (HV0.1) obtained for the group of samples treated with MI Varnish® were higher compared with the other two groups (p = 0.001 for both comparisons), while the first and third groups did not differ significantly from each other (p = 0.97). SEM analysis showed uneven patterns and porosities on all samples tested. EDS results showed an increase in the mineral content of the examined samples, with the highest mineral content observed in the MI Varnish® group. It can be concluded that MI Varnish® use has a better remineralization effect on enamel than the other two materials.