Background: In pulpectomy, to remove the inflamed or diseased pulp tissues and smear layer, the root canal is disinfected with mechanical instrumentation and copious irrigation. Aim: The purpose of this present study is to evaluate the antibacterial efficacy of etidronic acid as an irrigant in primary teeth. Materials and methods: A total of 60 necrotic primary teeth in children aged 3–8 years were included. Of these, 30 were irrigated with 2% chlorhexidine (CHX) gluconate (group I) and 30 with 9% etidronic acid (group II). Two microbiological samples were collected with sterile paper points from the canal in both groups during the pulpectomy process—first after access opening and before the first irrigation (S1), and second after instrumentation and final irrigation, before filling (S2). The presence of Enterococcus faecalis was determined using colony-forming units per milliliter (CFU/mL) in all samples (S1 and S2). Results: After analyzing the samples before and after irrigation in groups I and II, there was a statistically significant reduction in CFU/mL (p < 0.05). Group II had a statistically significant advantage when the two groups were compared after irrigation. Conclusion: As a result, etidronic acid can be recommended as a pulpectomy irrigating solution for necrotic primary teeth. © 2025 Elsevier B.V., All rights reserved.