Aim: To evaluate and compare the instrumentation time, obturation time, quality of obturation, and clinical and radiological success of pulpectomized teethfollowing root canal preparation of primary molars with rotary and manual file system. Methods: A total of 150 primary molars requiring pulpectomy were selected from children aged four to seven years. These teeth were divided into three groups of 50 teeth each. In Groups 1, 2, and 3, cleaning and shaping were carried out with Kedo-S pediatric rotaryfiles, HERO Shaper rotary files, and manual NiTi K-files, respectively. Obturation was carried out with zinc oxide eugenol cement and an engine-driven Lentulo spiral. The instrumentation and obturation times were recorded. A radiographic assessment of thequality of the root filling was carried out immediately after obturation. Finally, the pulpectomized teeth were clinically and radiographically evaluated over a two-year period. Results: The mean instrumentation times for Groups 1, 2, and 3 were 14.56 ± 2.89 min, 17.93 ± 3.51 min, and 29.00 ± 2.08 min, respectively. The mean obturation times for Groups 1, 2, and 3 were 8.11 ± 1.7 min, 7.93 ± 1.3 min, and 9.64 ± 17.61 min, respectively. The mean difference in the quality of obturation was not statistically significant in primary molars instrumented with Kedo-S pediatricand HERO Shaper rotary file systems (p = 0.16). However, this mean difference was significant when compared between primary molar instrumented with rotary file systems and manual NiTi files (p = <0.001). At two years, the clinical success rate was 100% and the radiological success rates were 95.3%, 97.9%, and 89.5% in Groups 1, 2, and 3, respectively. Conclusions: The rotary file systems took significantly less instrumentation and obturation time than the manual NiTi files. There were no significant differences in obturation quality or success rates after two years.