IntroductionEndodontic microsurgery is a very important technique for preserving the natural teeth. The outcomes of endodontic microsurgery largely depend on the skill and experience of the operators, especially for cases in which the apices are located far away from the labial/buccal cortical bone. A dynamic navigation system (DNS) could provide a more accurate and efficient way to carry out endodontic microsurgery. This study is devoted to comparing the clinical outcomes of the DNS technique with those of the freehand technique.Methods and analysisSixteen patients will be randomly assigned to one of two groups. For the experimental group, the osteotomy and root-end resection will be performed under the guidance of dynamic navigation. For the control group, these procedures will be performed freehand by an endodontist. The required time to perform these procedures will be used to evaluate the efficiency of the DNS technique. A Visual Analogue Scale will be used to evaluate pain at 1, 3 and 7 days after endodontic microsurgery. Preoperative and postoperative cone beam CT scans will be obtained to evaluate the accuracy of the DNS technique. The global coronal deviations, the apical deviations and the angular deflection will be measured. The root-end resection length deviation, the root-end resection angle deviations, the extent of the osteotomy and the volume change of the buccal cortical bone will also be measured. Periapical radiographs will be obtained to evaluate the outcome at 1 year after microsurgery. The time to execute the study, including follow-ups, will last from 1 June 2022 to 31 December 2025.Ethics and disseminationThe present study has received approval from the Ethics Committee of Peking University School and Hospital of Stomatology. The results will be disseminated through scientific journals.Trial registration numberChiCTR2200059389.