Background and Objectives: Rotary endodontics has been popularized over the time in an effort to shorten the treatment duration and improve the efficacy of the operator. The aim was to compare the efficiency of instrumentation time taken by manual K-files and rotary Protapers for cleaning the root canals in primary molars, followed by evaluation of obturation time clinically and quality of obturation radiographically. Results: The Protaper system presented shorter instrumentation time compared to the manual technique with K-files. The mean instrumentation time being 21.7 and 12.07 minutes for K-files and Protaper system respectively and the mean obturation time was 20.57 and 12.3 minutes respectively. Difference was proven statistically significant (p <0.001). However, for the quality of obturation even though 76.7 % of the canals showed optimal filling with protapers as compared to only 53.3 % with K-files, there wasn’t a statistical significant difference (p >0.05). Conclusion: Rotary in pediatric endodontics fared better in terms of instrumentation time and obturation time and quality than the manual instrumentation technique which can be a promising technique in pediatric endodontics as time is the poignant factor that plays a decisive role in impending cooperation of the child patients in coping with dental treatment.