Microorganisms play a crucial role in the development of pulpal and periapical infections, with Enterococcus faecalis (E. faecalis) being one of the most persistent pathogens found in root canal failures. Effective elimination of such microorganisms is essential for the success of endodontic therapy. Magnetized water, with its altered physicochemical properties, has recently emerged as a potential alternative root canal irrigant due to its increased alkalinity and reduced surface tension. This study aims to compare and evaluate the antimicrobial efficacy of magnetized water and normal saline against E. faecalis in primary teeth through an in vivo study. This will be in vivo study conducted on primary teeth indicated for pulpectomy in children. Pre- and post-irrigation microbial samples were collected from selected teeth and cultured on Brain Heart Infusion (BHI) agar to determine colony-forming units (CFUs) of E. faecalis. The teeth were randomly assigned to two groups: Group A (irrigated with magnetized water) and Group B (irrigated with normal saline). The reduction in microbial load was recorded and compared between the two groups.