Background: Root canal cleaning is a key step in the endodontic treatment of the primary molars. An innovative generation of endodontic instruments has been devised with the aim of emerging better procedures. The objective of the study is to assess the preparation of time, the risk of lateral perforation, and the removal of dentin from Kedo-S and Mtwo rotary instruments on primary teeth. Study design: This is an in vitro experimental study comparing the two groups. Materials and methods: A total of 50 extracted mandibular primary first molars are collected, divided randomly into two groups of 25 teeth each. Group I: Kedo-S Pediatric rotary file, Group II: Mtwo rotary file. Distal canal is standardized for evaluation and teeth are sectioned at the CEJ. The teeth were instrumented according to manufacturer's guideline. Both the groups are scanned before and after instrumentation of the canal using cone-beam computed tomography (CBCT) and values are evaluated. Results: Compared with Mtwo files, Kedo-S files need less instrumentation time and limited lateral perforation. No statistical differences were reported between the instrumentation of Kedo-S and Mtwo with regard to the amount of dentin removed. Conclusion: In pediatric endodontics, Kedo-S pediatric rotary file can be considered an effective alternative to traditional rotary files because it requires less instrumentation time and preserves dentin thickness.