The aim of this study was to evaluate the distance between the maxillary central incisor root and the incisive canal based on skeletal malocclusion classification and to analyze the morphology of the incisive canal using cone-beam computed tomography (CBCT). Skeletal malocclusion was categorized into Class I, II, and III using lateral cephalometric analysis. Measurements of the distance between the maxillary central incisor root and the incisive canal were taken at two levels: 2 mm (L1) and 4 mm (L2) superior to the labial cementoenamel junction of the maxillary central incisor. At L1, the distance was found to be closer in the Class II group compared to the Class I or Class III groups. Similarly, at L2, the Class II group exhibited a closer distance than the Class III group. Interestingly, females showed a closer distance compared to males at both L1 and L2. Further analysis revealed a significant gender difference in the Class I and III groups, but not in the Class II group. These findings emphasize the significance of evaluating the distance between the maxillary central incisor root and the incisive canal in patients with skeletal Class II malocclusion, regardless of gender.