Dens invaginatus is a morphological abnormality of the tooth in which the coronal tooth enamel and dentin fold inwards towards the pulp cavity. Dens invaginatus type III (Oehlers: 1957) is characterized by infolding of the enamel and dentin as far as the root apex. This report describes a case of surgical and non-surgical endodontic therapy for a maxillary lateral incisor with type III dens invaginatus, necrotic pulp, and an associated large periradicular lesion. The patient was a 16-year-old man. Periapical radiographs suggested the presence of an untreated area of invagination. Cone beam computed tomography (CBCT) was then used for three-dimensional observation of the morphological details of this area. The CBCT scans revealed invagination and its relationship with the pulp chamber. A dental operating microscope was used to access two primary root canals and the area of invagination. The root canals were then localized, negotiated, enlarged, and filled with calcium hydroxide. Two months later, the canal and invagination were obturated with core-based gutta-percha (FlexPoint Neo: FP core-carrier technique) and restored. Cone beam computed tomography and microscopic techniques allow even complicated cases of dens invaginatus to be diagnosed and treated using non-surgical root canal management.