Purpose: The purpose of this study was to evaluate the effect of 2% chlorhexidine gluconate (CHX) compared to normal saline solution (NSS) as an irrigant during pulpectomy in primary molars. Methods: Sixty-four primary mandibular molars from 42 children (average age=5.29±1.45 years old) met the inclusion criteria. CHX or NSS was allocated to each tooth by stratified block randomization. A 1-visit pulpectomy and stainless steel crown were performed by a single investigator. The clinical and radiographic diagnoses were blindly assessed by 2 calibrated investigators. Results: The overall success rates in the NSS group were approximately 83%, 93%, and 97% at 6, 12, and 18 months, respectively. In the CHX group, the overall success rates were 100%, 97%, and 93% at 6, 12, and 18 months, respectively. Using the chi-square test, the outcomes were significantly different at 6 months, but not significant at 12 and 18 months. Conclusions: The use of 2% chlorhexidine gluconate in primary molar pulpectomies might enhance the outcome of the treatment 6 months postoperatively. Both normal saline solution and CHX irrigants gave comparable results at longer postoperative periods.