Introduction: The adequate knowledge of the canal configuration can improve the quality and prognosis of endodontic treatment. The aim of the study was to determine the frequency of C-shaped root canal in the mandibular permanent second molars among a Pakistani subpopulation sample by utilizing cone-beam computed tomography images. Materials and Methods: Cone-beam computed tomographic images of 360 patients with 720 mandibular second molars were analyzed for the presence of C-shaped canal configuration. The root canal system was classified according to Fan's classification at three distinct levels. Unilateral or bilateral presence of C-shaped root canals and the location of the longitudinal groove were assessed. Moreover, the correlation of frequency of C-shaped canal with the gender was measured using the Chi-square test. The data were analyzed using SPSS version 23. Results: Of 720 mandibular second molars of 360 patients, 10% of teeth were found to have C-shaped canals in 48 patients. The most commonly noted C-shaped canal configurations in the coronal and middle third were C1 (41.7%) and C3 (37.5%), respectively, whereas C2 (33.3%) and C4 (33.3%) configurations were commonly found in the apical third. Twenty-four of 48 patients had bilateral C-shaped root canals. Overall, 37.5% of the teeth were right-sided teeth and 62.5% were left-sided teeth. The frequency of C-shaped canals was significantly higher in females as compared to males, 15.6% and 4.2%, respectively (P = 0.03). The longitudinal groove was most commonly located on the lingual surface (66.7%). Conclusions: The frequency of C-shaped canal configuration in the Pakistani subpopulation was 10% in the mandibular second molar teeth.