Various rotary endodontic instruments were used and studied for the root canal preparation of the primary teeth. Recently, a new venture evolved in the field of pediatric endodontic, which was Kedo S rotary files. These are the files designed exclusively for root canal preparation of the primary teeth. Aim: The study aimed to comparatively evaluate the dentin removal and taper of root canal preparation of Hand K files, Rotary Prosper files, and Rotary Kedo S files using cone-beam computed tomography (CBCT) and instrumentation time using stopwatch in primary molars. Materials and methods: Sixty-three root canals of maxillary and mandibular primary molars were included in the study. The root canals were randomly assigned to Hand K file (group I), Rotary ProTaper file (group II), and Rotary Kedo S file (group III). Dentin removal and taper of the root canal preparations were evaluated by using CBCT. Results: All the three file systems do not show any statistical significant differences at middle third and apical third but at coronal third, Kedo S removed significantly less amount of dentin as compared to the Hand K file. Taper of the preparations did not show significant differences, even though the rotary files showed good taper in maximum number of root canals. Conclusion: Although not much statistical significant differences were observed in our study, the rotary file system performed slightly better in root canal preparations in primary molars.