Introduction: Pediatric Endodontics was bestowed with rotary instruments by Barr et al., in 2000. It enhances the quality of obturation and reduces instrumentation time by providing conical shape to the root canal. The aim of this study was to compare instrumentation time and quality of obturation of manual instrumentation and two rotary systems in the preparation of primary molar root canals. Method: A randomized control trial where pulpectomy was performed on 30 primary molars equally distributed for instrumentation with Hand K files, rotary Kedo SG files and rotary Protaper Gold files. The instrumentation time and obturation quality were noted. Results: Kedo–SG files showed the least instrumentation time whereas the best quality of obturation was seen with Protaper Gold Rotary files as compared to hand files (P < 0.001) Conclusion: Pediatric rotary files Kedo–SG files reduce instrumentation time whereas Protaper Gold rotary files produce improved obturation quality.