To determine the correlation between the quality of root canal obturation and postoperative pain following root canal preparation with rotary and manual file systems in the primary molars. A total of 150 primary molars requiring pulpectomy were selected from children aged 4–7 years. The selected teeth were divided into three groups: Kedo-S (KS), HERO Shapers (HS) and Manual Files (MF)-of 50 teeth each. In groups KS, HS, and MF, root canal instrumentation was carried out with Kedo-S pediatric rotary files, HERO Shaper rotary files, and manual NiTi K-files, respectively. Root canal obturation was carried out with zinc oxide eugenol cement using an engine-driven Lentulo spiral. The quality of the root filling was radiographically assessed immediately after obturation. The postoperative pain was evaluated at time intervals of 6, 12, 24, 48, 72 h, and 1 week. The quality of obturation was superior in the root canals instrumented with rotary file systems compared to manual files. There was decreased postoperative pain with the use of rotary file systems as compared to manual files. In all three groups, postoperative pain decreased over time. The use of rotary file systems resulted in a higher percentage of optimal root canal filling with lesser postoperative pain than the manual file system. The overfilled root canals were not associated with significant postoperative pain.