Aim: To perform a systematic review comparing the canal-shaping ability of WaveOne and ProTaper rotary using cone-beam computed tomography (CBCT) and to evaluate the file that provides better performance clinically. Materials and methods: The eligibility criteria selected for the study was based on the population intervention comparison outcome(s) study (PICOS). Using different search strategies from the keywords and their combinations, English language articles only between January 1, 2009, and October 31, 2019, from electronic biomedical journal databases were obtained. In vitro studies comparing the canal-shaping ability of ProTaper and WaveOne file systems using the CBCT method were included. Total 137 articles were reviewed out of which 61 articles were excluded during title screening as they did not meet the motive of our study. Total 76 articles were screened for duplicates and 63 articles were excluded. A total of 13 articles were selected for reviewing abstract and full text. Total 13 relevant articles were selected for final synthesis. The pilot Microsoft Excel sheet was filled with the relevant data that matched the study. Review results: Total 13 relevant articles were selected for final review. The file systems were compared based on two main parameters such as the apical transportation caused and the ability of the file to remain centered within the canal. We found significant differences in these two parameters when the WaveOne reciprocating file system was compared with the ProTaper rotary file system. A definite conclusion could be drawn that the WaveOne reciprocating file system was better in shaping the canal. Conclusion: Based on the results, the canal-shaping ability of the WaveOne reciprocating file system was better than the ProTaper rotary file system. Clinical significance: Clinically, the canal-shaping ability determines the performance of a particular file system and CBCT is the most effective 3-D mode to determine the centering ratio and apical transportation caused. Thus, further comparative studies between these two file systems using CBCT with larger sample size and with elaborate search strategies are required for better result.