Statement of Problem: Canal preparation is one of the most important and time- consuming steps in endodontic treatment of primary teeth. Regarding the difficulties in behavior management of some children, rotary (nickel-titanium) files proved more facilities and speed and hence more success in the root canal treatment of primary teeth.Purpose: The purpose of the present study is comparison of the success rate and cleaning time of pulpectomy in necrotic primary molar teeth using manual and rotary instruments.Materials and Methods: In this study which is an interventional in vivo clinical trial, 40 patients, mean age 5.7+0.92, were randomly selected and divided into two equal groups (I, II). In the first visit, pulpotomy of the necrotic teeth was done for all of the cases. In the second appointment after local anesthesia and isolation of the teeth with rubber dam, preparation of the canals was done with pro-taper nickel-titanium files (S1, S2, F2) in the first group and with stainless steel manual K-files (10-30) in the second group. The total time needed for debridement was calculated exactly by chronometer. The canals were then filled with ZOE by using lentulo spirals and periapical radiography was prepared for all of the cases. The patients were followed-up in 3 and 6 months intervals and the statistical analysis were done by Non-Parametry Mann-Whitney test.Results: The success rates of manual and rotary instruments were 85% and 90% respectively after 3 months. The success rate of the two groups (I, II) was 100% after 6 months follow-up and all of the signs and symptoms including pain, abscess, fistula and perapical radiolucency disappeared. The time needed for canal preparation was calculated 4.12 minutes (251.75+32.58 seconds) with Pro-Taper and 9.21 minutes (563.05+ 70.03 seconds) with manual instruments. The difference was statistically significant.Conclusion: The success rate of manual and rotary instruments was 100% in both groups but the preparation time (which is an important clinical factor for patients management) significantly reduced using rotary instruments. Hence, pulpectomy of the primary teeth using rotary instruments (Pro-Taper files) is recommended for root canal treatments in children.Key words: Pulpectomy, Primary Molar Teeth, Pro-Taper file, K-file