The aim of this study was to evaluate the effect of Er:YAG laser irradiation on the micro-shear bond strength of self-etch adhesives to the superficial dentin and the deep dentin before and after thermocycling. Superficial dentin and deep dentin surfaces were prepared by flattening of the occlusal surfaces of extracted human third molars. The deep or superficial dentin specimens were randomized into three groups according to the following surface treatments: group I (control group), group II (Er:YAG laser; 1.2 W), and group III (Er:YAG laser; 0.5 W). Clearfil SE Bond or Clearfil S-3 Bond was applied to each group's dentin surfaces. After construction of the composite blocks on the dentin surface, the micro-shear bond testing of each adhesive was performed at 24 h or after 15,000 thermal cycles. The data were analyzed using a univariate analysis of variance and Tukey's test (p < 0.05). Laser irradiation in superficial dentin did not significantly affect bond strength after thermocycling (p > 0.05). However, deep-dentin specimens irradiated with laser showed significantly higher bond strengths than did control specimens after thermocycling (p < 0.05). Thermocycling led to significant deterioration in the bond strengths of all deep-dentin groups. The stable bond strength after thermocycling was measured for all of the superficial-dentin groups. No significant difference was found between the 0.5 and 1.2 W output power settings. In conclusion, the effect of laser irradiation on the bond strength of self-etch adhesives may be altered by the dentin depth. Regardless of the applied surface treatment, deep dentin showed significant bond degradation.