The endodontic preparation of curved and narrow root canals is challenging. Aggressive preparation of the root canal with rotary file systems may result in canal transportation and excess removal of dentine, a major reason for poor prognosis of root canal treated tooth. The purpose of the present study was to compare the canal transportation and centering ability of Rotary ProTaper Next (PTN) and HyFlex EDM file systems using cone beam computed tomography (CBCT) in curved root canals. Forty extracted human mandibular first molars were mounted on acrylic blocks. Specimens were divided into two groups: Group PTN (ProTaper Next) and Group HF (HyFlex EDM). Mesiobuccal canals were instrumented with ProTaper Next and HyFlex EDM rotary files. Pre-instrumentation and Post-instrumentation scans were performed using CBCT under similar conditions. Canal transportation, centering ratio and volume of the dentine removed were evaluated at 3 cross-section levels; 3-mm, 6-mm and 9- mm from the root apex. The data were statistically analyzed and the level of significance was set at p ≤ 0.05.Canal transportation was seen minimal with HyFlex EDM (0.021±0.009) at 3mm from the apex and maximum with ProTaper Next (0.028±0.021) at 9mm from the apex. Mean centering ratio was lower for HyFlex EDM to ProTaper Next at all levels. Both Pro Taper Next and HyFlex EDM systems shaped the canals with adequate centering ability and minimal canal transportation. Hyflex EDM better maintained canal centricity but the difference was not statistically significant.