Few reports have addressed the effects of diode laser irradiation at 980 nm on the morphology and fracture resistance of dentine. The purpose of this study is to evaluate the effects of 980-nm diode laser on the ultrastructure and fracture resistance of root dentine. The roots of 90 extracted canine teeth were divided into three groups according to the type of irrigating solution (water, NaOCl, and NaOCl/EDTA) and subdivided into three subgroups (n = 10) according to the amount of laser irradiation (without irradiation, 1.5 W/100 Hz and 3.0 W/100 Hz). The roots were filled with an epoxy resin-based sealer and gutta-percha and then subjected to a fracture resistance test. Data were analyzed by ANOVA and the Tukey test (p < 0.05). Additionally, 18 canine teeth were prepared using the same irrigation/irradiation protocols and evaluated by scanning electron microscopy (SEM). The SEM showed greater changes when the laser power increased, and the changes also varied according to the irrigating solution. A modified smear layer was observed in specimens that were treated with water and then laser-irradiated. The laser treatment did not alter the fracture resistance of roots treated with 1.5 W/100 Hz (246.3 ± 29.5 N) and 3.0 W/100 Hz (215.3 ± 25.1 N) laser power. The roots treated with NaOCl were more susceptible to fracture (199.4 ± 15.1 N) than those irrigated with water (254.2 ± 23.0 N) (p < 0.05). The 980-nm diode laser altered the morphology of the dentine but did not affect the fracture resistance of the roots.