Objective: The proposed study aims to compare the effectiveness of conventional endodontic treatment (ET) with that of ET associated with antimicrobial photodynamic therapy (aPDT) in patients with apical lesion.Methods: Controlled, double-blind, randomized clinical trial (RCT); superiority study with three parallel arms. Randomization will be conducted in exchange blocks of six, with allocation 1:1:1. The control group will receive conventional ET, while experimental group 1 (EG1) will receive conventional ET + aPDT with laser at 660 nm, fluence of 600 J/cm2; EG2 will receive conventional ET + aPDT with laser at 660 nm, fluence of 1200 J/cm2. The primary outcome will be canal disinfection before treatment, measured by analysis of colony formation (CFU/mL) and the success rate measured after 6 months on the clinical and radiographic evaluations. The mean and standard deviation will be calculated for continuous outcomes, and the CFU/mL mean between groups will be evaluated by ANOVA test. The Chi-squared test will be calculated for binary outcomes. A logistic regression analysis will be performed to assess differences in the success rate between groups, adjusted for the covariates. The Stata 18 software will be used, with a significance threshold of 5%.Conclusions: Few RCTs have evaluated the effectiveness of aPDT in root canal disinfection in patients with permanent dentition presenting apical lesion. New RCTs with larger numbers of participants are needed to support using aPDT as an adjuvant to conventional ET in root canal disinfection for routine use in clinical practice. The trial was registered prospectively in ClinicalTrials.gov (NCT05916859).