Background: This systematic review and meta-analysis aimed to determine whether reciprocating file systems reduce postoperative pain more effectively than rotary file systems. Materials and methods: This review followed the preferred reporting items for systematic review guidelines to ensure rigorous and transparent reporting. The databases searched included MEDLINE, Cochrane Library, and Google Scholar, targeting articles published in English between January 2000 and April 2024. Randomized controlled trials involving children aged 4–12 years requiring pulpectomy, comparing reciprocating file systems with rotary systems. Outcomes included quality of obturation, instrumentation time, and postoperative pain. The participants, settings, interventions, comparators, outcome measures, study designs, statistical analyses, results, and all other relevant data were meticulously and accurately extracted from all included studies. Data extraction was performed and recorded in Excel sheets, with separate documentation maintained for each primary outcome. Results: Out of 279 studies initially identified, 272 were excluded due to duplication, non-English language, or not meeting criteria. Seven studies that met the necessary criteria were included in the systematic review. Among them are five comparisons for instrumentation time, four for postoperative pain, and two comparisons for quality of obturation. Results of the meta-analysis showed that instrumentation time was lower in the rotary file systems than in reciprocating file systems. Postoperative visual analogue scale (VAS) scores after 6 hours and 24 hours were almost similar among both file systems. Conclusion: Given the limitations of this review, it can be said that the postoperative pain scores were comparable between reciprocating and rotary file systems. The root canal preparation time was significantly shorter with the reciprocating system compared to the rotary system. Clinical significance: In pediatric dentistry, behavior management plays a vital role in successful treatment. Therefore, opting for the correct file system is fundamental and helps in minimizing pain and instrumentation time, thereby enhancing the overall patient experience.