Aim: To compare and evaluate the efficacy of ProTaper^® Universal retreatment system (URS) files in retrieval of gutta-percha (GP) from the canals obturated with two different obturation techniques, using cone-beam computed tomography (CBCT). Materials and methods: Fifty-two extracted maxillary central incisors fulfilling inclusion criteria were decoronated and prepared with ProTaper^® rotary files till F3 file size. Specimens were randomly divided into two groups and were obturated with GP. The first group was obturated with cold lateral condensation technique and second group was obturated with thermoplasticized GP technique. The root fillings were retrieved from the canals using ProTaper^® URS files. Preoperative and postoperative CBCT imaging was employed to assess the residual filling material in the canals. ITK-Snap software was used to calculate volume of filling material in the canals. Data were entered into Microsoft excel worksheet and analyzed using Statistical Package for Social Sciences, version 18.0 (SPSS Inc., Chicago, IL, USA). Descriptive statistics with percentage mean and standard deviation was computed. Independent sample t test was used to test the difference between study groups. Results: Residual root canal fillings were detected in all specimens. The mean volume percentage of remaining filling material was 10.69% ± 3.50 and 13.70% ± 3.63 in canals obturated with cold lateral condensation and thermoplasticized GP techniques, respectively. Conclusion: This study concluded that though ProTaper^® URS failed to remove GP completely, it was more efficient in the group of root canals obturated with cold lateral condensation than the canals obturated with thermoplasticized GP technique.