Background: The present study was conducted to compare manual vs rotary instrumentation in molar pulpectomy in children. Materials & Methods: The present study was conducted on40 children age ranged 4- 10 years of both gender. Patients were divided into 2 groups. Group I (N = 20): The root canals were instrumented with manual files as per manufacturer’s recommendation. Group II (N = 20): the root canals were instrumented with rotary. A postobturation radiograph was taken to assess the quality of obturation. Results: The mean instrumentation time in group I was 25.7 minutes and I group II was 19.2 minutes. Obturation time in group I was 5.6 minutes in group I and 4.2 minutes in group II. The difference was significant (P< 0.05). Quality of obturation was under fill in 16% in group I, 13% in group II, optimal 58% in group I, 60% in group II, over fill 26% in group I, 27% in group II The difference was significant (P< 0.05). Conclusion: Authors found that there was significant less instrumentation and obturation time in rotary instrumentation than manual instrumentation.