Background <p>This study was conducted to evaluate the registration accuracy of an intraoral scan-assisted registration (IR) method for guided endodontics.</p> Methods <p>Seventy teeth were mounted into five stone dentition models. In terms of the registration method, there were two groups: one utilizing U-shaped tubes for registration (UR group) and the other using an intraoral scanner to aid in registration (IR group). In the UR group, U-shaped tubes were fixed on the model. Preoperative cone-beam computed tomography (CBCT) scans were performed, and fiducial markers on the U-shaped tubes were extracted for registration. In the IR group, fiducial markers were fixed on the crowns after preoperative CBCT scans were performed. The point cloud data were obtained by an intraoral scanner and aligned with the CBCT image to unify the coordinates of the model and markers. The markers were subsequently extracted for registration. The fiducial registration error (FRE) and target registration error (TRE) were calculated to evaluate the registration accuracy. The linear and angular deviations in the accuracy of root canal orifice localization under dynamic navigation were compared and analyzed using the two registration methods. Data were analyzed using t tests and repeated measures analysis of variance (ANOVA) for normally distributed data and the Mann–Whitney U test for nonnormally distributed data.</p> Results <p>The TRE of the IR (0.24 ± 0.09&#xa0;mm) was lower than that of the UR (0.37 ± 0.08&#xa0;mm), which was reflected mainly in the posterior teeth (<i>P</i> &lt; 0.001). No significant difference in the accuracy of the linear or angular deviation was observed between the two groups (<i>P</i> &gt; 0.05).</p> Conclusions <p>Within the limitations of this in vitro study, the IR was an accurate registration method in guided endodontics. However, further clinical validation is needed before this technique can be used in clinical practice.</p>