In this case report, we present the endodontic treatment and microsurgical intervention of dens invaginatus affecting a lateral incisor using cone-beam-computed tomography (CBCT). A 26-year-old woman visited us with a diagnosis of acute apical periodontitis in the upper right lateral incisor (tooth 12). Endodontic treatment of the tooth was carried out. Intraoral radiography provided limited information on the unusual anatomy of the pulp chamber and root canal system; therefore, preoperative CBCT was performed. At the 3-month recall, a radiograph revealed a 5-mm-diameter lateral transparency, and CBCT was, therefore, repeated to facilitate microsurgery treatment planning. A medical image-processing program was used to demonstrate the changes between the CBCT images obtained before and after root canal preparation. In conclusion, endodontic treatment of dens invaginatus is challenging even for endodontic specialists, because the therapy sometimes requires surgical intervention. The currently available novel three-dimensional imaging modalities may have importance in planning and following up the root canal treatment in such cases, especially when unforeseen complications arise.