This study evaluated the effects of fluoride on subsurface enamel demineralization induced by two commonly used chemical models. Forty-eight enamel blocks were demineralized at pH = 5.0 by an acetate buffer (Group 1), a lactate buffer (Group 2), an acetate buffer with 0.02 ppm fluoride (Group 3) and a lactate buffer with 0.02 ppm fluoride (Group 4) at 25 °C for 3 weeks. The surface destruction percentage (SDP), mineral loss and lesion depth of the blocks were studied using micro-computed tomography. An elemental analysis of the enamel surface was evaluated using an energy-dispersive X-ray spectroscopy. Surface micro-hardness was determined by the Knoop Hardness Test. The mean lesion depth of Groups 1 through 4 were 134.1 ± 27.2 µm, 96.1 ± 16.5 µm, 97.5 ± 22.4 µm and 91.1 ± 16.2 µm, respectively (p < 0.05; group 1 > 2, 3 > 4). The SDPs of groups 1 through 4 were 7.8 ± 8.93%, 0.71 ± 1.6%, 0.36 ± 1.70% and 1.36 ± 2.94% (p < 0.01; group 1 > 2, 3, 4). The fluoride in mean weight percentages of groups 1 through 4 were 1.12 ± 0.24%, 1.10 ± 0.20%, 1.45 ± 0.40% and 1.51 ± 0.51%, respectively (p < 0.01; group 3,4 > 1,2). The mean Knoop hardness values of groups 1 through 4 were 27.5 ± 13.3, 39.7 ± 19.3, 73.6 ± 44.2 and 91.0 ± 57.2, respectively (p < 0.01; group 4 > 3 > 2 > 1). The chemical model using an acetate buffer solution created significantly deeper zones of subsurface demineralization on enamel than the lactate buffer solution. An acetate buffer may damage the enamel surface, but the surface damage can be prevented by adding fluoride.