Introduction The endodontic treatment of primary teeth presents considerable complications due to their distinct anatomical properties. In order to achieve a successful endodontic treatment, certain factors must be assessed. These factors include a precise diagnosis, thorough cleaning, and a reliable disinfection protocol. Although sodium hypochlorite (NaOCl) has been effective as an irrigation agent in primary teeth, it is important to recognize that higher concentrations of NaOCl might possibly inflict toxic harm on the periapical environment if they penetrate the tooth's apical foramina. Since primary teeth are important, pediatric dentists must choose an appropriate NaOCl concentration for root canal irrigation, as higher concentrations can be toxic. Thus, the current investigation examined the cytotoxicity of two different NaOCl concentrations at various volumes. Methods To evaluate the cytotoxicity potential, a culture ofnauplii (brine shrimp) was prepared and subjected to testing. For the test, 5, 10, 20, and 40 µL of 1% and 3% NaOCl were added to the brine shrimp culture at different concentrations, and saline was used as a control. After a span of 24 hours, the total number of alive nauplii was duly noted. Results After 24 hours, nauplii showed no mortality in the control group. For 1% NaOCl, mortality ranged from 10% to 20% across volumes, with no significant differences (p = 0.193). In contrast, 3% NaOCl caused significantly higher mortality: 20% at 5 µL, 30% at 10 and 20 µL, and 60% at 40 µL (p = 0.007). Tukey's analysis revealed no significant differences for 1% NaOCl (p > 0.05) but significant differences for 3% NaOCl at 40 µL (p < 0.05). Conclusion Based on the results of the present study, it was observed that a 1% NaOCl solution exhibited a lower level of toxicity in comparison to a 3% NaOCl solution. These findings highlight the importance of using lower concentrations of NaOCl for endodontic irrigation in pediatric dentistry to reduce the risk of tissue damage and ensure safer outcomes for young patients.