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To determine and compare the accuracy and efficiency of a dynamic navigation system (DNS) with a freehand (FH) technique when conducting root-end resection in a human cadaver model.Forty roots in cadaver heads were included and divided into two groups: DNS (n = 20) and FH (n = 20). Cone beam computed tomography (CBCT) scans of all teeth were taken. The drilling path and depth were planned virtually to using the X-guide software (X-Nav Technologies, Lansdale, PA, USA). Osteotomy and root-end resection were done under navigation in the DNS group, and freehand under the dental operating microscope in the FH group. Post-operative CBCTs were taken. Linear deviations, angular deflection, time of operation and number of mishaps were compared with determine the accuracy and efficiency. Shapiro-Wilk, one-way ANOVA and Fisher exact tests were used (P 0.05).Linear deviations, angular deflection and operation time were significantly less in the DNS group (P 0.05). The number of mishaps was not different between the two groups (P 0.05). Subgroup analyses revealed that the distance of5 mm from buccal cortical plate was significantly associated with lower accuracy, increased operation time and greater incidence of mishaps in the FH group (P 0.05), but not in the DNS group.The dynamic navigation system was more accurate and more efficient in root-end resection in a cadaver model than the freehand technique. The distance of the roots from the buccal cortical plate had a significant negative impact on the accuracy and efficacy of the root-end resection procedure when using the freehand technique. The dynamic navigation system has the potential to be a safe and reliable technological addition to endodontic microsurgery.