Sodium hypochlorite (NaOCl) is widely utilized in endodontics for its effective antimicrobial properties and ability to dissolve necrotic tissues. However, its use is not devoid of risks, including potential severe tissue damage and chemical burns. This systematic review evaluates the documented risks of using NaOCl in endodontic treatments. It compares its safety and efficacy with other endodontic irrigants, such as EDTA and chlorhexidine. This review followed the "Preferred Reporting Items for Systematic Reviews and Meta-Analyses" guidelines and registered with PROSPERO. Comprehensive searches were performed in PubMed, Scopus, Web of Science, and CENTRAL databases, with additional hand searches in grey literature. Studies were selected reporting adverse effects related to NaOCl used in endodontic procedures, ranging from randomized controlled trials to case reports. Data extraction and risk of bias assessment were systematically performed using standardized tools. Seventeen studies were included, detailing instances from chemical burns to severe allergic reactions and tissue necrosis associated with NaOCl use. The risk of bias was predominantly low across the studies. Sodium hypochlorite demonstrated a higher efficacy in microbial eradication and tissue dissolution than other irrigants, though it also showed a higher incidence of severe complications when mishandled. Sodium hypochlorite remains a cornerstone in endodontic disinfection due to its potent antimicrobial and tissue dissolution properties. However, its application must be meticulously managed to prevent complications. Future research should focus on optimizing concentrations and application techniques to enhance safety and effectiveness, potentially integrating safer alternatives or complementary solutions like EDTA to mitigate risks while preserving irrigant benefits.