Cone-beam computed tomography (CBCT) is a useful diagnostic tool for identification of both internal and external root configurations. This case report describes the endodontic management of a lateral incisor with both dens invaginatus and external root irregularity by using CBCT. Nonsurgical endodontic retreatment was performed on the lateral incisor with dens invaginatus. A perforation through the dens invaginatus and external concavity was repaired using mineral trioxide aggregate. After 18 mon of follow-up, there were no clinical symptoms. Recall radiographs appeared normal and showed healing of the periapical pathosis. The understanding of both internal root canal configuration and external root irregularity using CBCT can ensure predictable and successful results.