The aim of endodontic therapy is to use various antimicrobial medications for proper cleaning and shaping to create an environment free of microorganisms by eradicating as many as possible from the root canal space. Even although it is a gold standard irrigant, sodium hypochlorite (NaOCl) is known for its cytotoxic effects on vital periapical tissues, making its higher concentrations inappropriate for use in conditions such as wide, underdeveloped, or damaged apices and in cases of perforations. Consequently, if it is ascertained that a gel form of sodium hypochlorite has equivalent antibacterial activity to the aqueous solution form, it could be employed in such situations. The aim of this study was the microbiologic evaluation of 5.25% sodium hypochlorite gel and aqueous solution as root canal disinfectants in multirooted teeth with primary endodontic lesions. Following ethical approval and CTRI registration, 42 patients who gave their consent and had multirooted teeth with pulpal necrosis and asymptomatic apical periodontitis were considered for the study. Following the opening of the access, pre-endodontic build up in case of class-II cavities and working length determination, a pre-operative sample (S1), which was regarded as the pre-operative microbial load of that canal, was acquired from the largest canal using a sterile paper point while maintaining strict isolation and disinfection. The computer randomization approach was used to divide the teeth into two groups at random just before beginning of chemo-mechanical preparation: Group A (n = 21)—canal disinfection with 5.25% sodium hypochlorite gel; Group B (n = 21)—canal disinfection with 5.25% sodium hypochlorite aqueous solution. Following the canal disinfection, a post-operative (S2) sample which was regarded as the postoperative microbial load of that canal was collected from the same canal using a sterile paper point. The Colony-Forming Units (CFUs) for the S1 and S2 samples were determined after 48 h aerobic incubation on Brain Heart Infusion (BHI) agar plates. The patients and the microbiologist were blinded throughout the procedure. Using SPSS 20.0 software (USA), the Shapiro–Wilk test and the Lilliefors Significance Correction were used for normality, followed by the Mann–Whitney U test which was used to compare the CFU difference (×105) between the two groups. A p value of <0.05 was perceived as statistically significant. The mean colony-forming units count difference between the 5.25% sodium hypochlorite gel and aqueous solution groups did not differ in a manner that was statistically significant (p = 0.744). In multirooted teeth with primary endodontic lesions, the 5.25% sodium hypochlorite gel and the aqueous solution demonstrated comparable antimicrobial effectiveness when implemented as root canal disinfectants.