Abstract Background The clinician should have complete knowledge of the normal anatomy of the root as well as complexities in the root canal configuration for a better outcome, as missed or improper handling of the canal system can lead to the failure of an entire endodontic procedure. The present study aims to assess the morphology of roots and canals in permanent mandibular premolars in the Saudi subpopulation with a new classification system. Methods The present study includes 1230 mandibular premolars (645 first premolars and 585-second premolars) from 500 CBCT images of the patients, including retrospective data. iCAT scanner system (Imaging Sciences International, Hatfield, PA, USA) was used to obtain the images; scanning of 8 × 8 cm images was performed at 120 KVp and 5–7 mA with a voxel size of 0.2 mm. The new method of classification presented by Ahmed et al. 2017 was used to record and classify the root canal morphology, followed by recording the differences regarding the age and gender of the patients. Comparison of canal morphology in lower permanent premolars and its association with gender and age of the patients was done by Chi-square test/ Fisher exact test; the significance level was set at 5% (p ≤ 0.05). Results The left mandibular 1st and 2nd premolars with one root were 47.31%, with two roots were 2.19%. However, three roots (0.24%) and C-shaped canals (0.24%) were reported only in the left mandibular 2nd premolar. The right mandibular 1st and 2nd premolars with one root were 47.56%, with two roots were 2.03%. The overall percentage of the number of roots and canals in the first and second premolars ¹ PM ¹ (88.38%), ² PM ¹ B ¹ L ¹ (3.5%), ² PM B ¹ L ¹ (0.65%), ¹ PM ^1–2−1 (3.08%), ¹ PM ^1–2 (3.17%), ¹ PM ^{1–2−1–2} (0.24%), ³ PMMB ¹ DB ¹ L¹ (0.48%). However, the C-shaped canals (0.40%) were reported in right and left mandibular second premolars. No statistically significant difference was reported between mandibular premolars and gender. A statistically significant difference was reported between mandibular premolars and the age of the study subjects. Conclusion Type I (¹ TN ¹) was the major root canal configuration in permanent mandibular premolars, which was higher among males. The CBCT imaging provides thorough details about the root canal morphology of lower premolars. These findings could support diagnosis, decision-making, and root canal treatment, for dental professionals.