Aim The aim of this systematic review was to answer the following question: in patients with primary endodontic infection, is there a statistically significant difference in the endotoxin levels after chemomechanical preparation with sodium hypochlorite (NaOCl) or chlorhexidine (CHX)? Methodology A protocol was prepared and registered on PROSPERO (CRD42017069996). Four electronic databases (MEDLINE via PubMeb, Scopus, Web of Science and Cochrane Library) were searched from their start dates to 1 March 2017 using strict inclusion and exclusion criteria and reviewed following PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) guidelines. Only clinical trials (randomized and nonrandomized) that compared the effectiveness of NaOCl and CHX to reduce endotoxins during chemomechanical preparation of teeth with primary endodontic infection were included. Two reviewers independently assessed the eligibility for inclusion, extracted data and assessed the quality using the risk of bias tool. Results From 712 articles that resulted from the initial search, 37 studies were included for full-text appraisal; four studies met the inclusion criteria for quantitative synthesis. A single meta-analysis was performed to compare the endotoxin levels before and after chemomechanical preparation with NaOCl or CHX. The forest plot of lipopolysaccharide (LPS) levels indicated that the data were heterogeneous [I-2 = 63.9%; Tau(2) = 574.5 (P = 0.04)]. The use of NaOCl and CHX during chemomechanical preparation significantly reduced the LPS levels compared to the initial ones. Conclusions Chemomechanical canal preparation with both NaOCl and CHX reduced the endotoxin levels compared to the initial ones found in primary endodontic infections. When NaOCl was used during chemomechanical preparation, endotoxins levels were lower than those obtained after chemomechanical preparation with CHX Ver menos