The successful outcome of endodontic therapy is intrinsically linked to a comprehensive understanding of root canal anatomy and its frequent variations. The objective of this study was to evaluate the root and root canal morphology of permanent maxillary and mandibular canines in a Saudi subpopulation from the Al-Baha region using cone-beam computed tomography (CBCT), specifically investigating the prevalence of Vertucci classifications and canal shape variations across different root levels. This retrospective study analyzed 120 CBCT scans of permanent canines. Internal anatomy was categorized according to Vertucci’s classification, and cross-sectional canal shapes were assessed at the cervical, middle, and apical thirds using a standardized 10-point scale. Data were analyzed using Chi-square tests and multivariate logistic regression to assess statistical significance (P < 0.05) by gender and dental arch. All examined teeth were single-rooted. While Vertucci Class I was the most prevalent configuration overall, mandibular canines exhibited significantly greater morphological complexity in the middle third than maxillary canines (P = 0.016), including an 8.5% prevalence of Class III configurations. Morphologically, the most frequent transition in canal shape was from oval at the cervical level to circular at the apical third. This CBCT-based analysis demonstrates that, although single canals predominate, mandibular canines in this subpopulation exhibit significant internal complexity and anatomical variation. These findings underscore the necessity for clinicians to utilize advanced imaging and adapt disinfection protocols to address the specific morphological transitions—such as oval-to-circular shapes and Class III configurations—identified in the mandibular arch to improve endodontic outcomes.