Dens invaginatus (DI) represents an endodontic challenge because of its complex root canal morphology. This case report presents the clinical management of a 22-year-old woman with type II DI in right maxillary lateral incisor with a painful swelling. Pulp testing revealed no response with the tooth. Type II DI with open apex and large periradicular lesion was seen on radiograph. The treatment was planned by using cone-beam computed tomography (CBCT) imaging. Canal treatment was completed in two appointments with the aid of a dental operating microscope. In the first appointment, the internal anatomy was modified using an ultrasonic tip, and chemo-mechanical preparation was performed using the XP-endo Finisher instrument and NaOCl; calcium hydroxide intracanal dressing was used for one month. In the second appointment, an apical plug of mineral trioxide aggregate (MTA) Repair HP was performed and the remaining pulp space was then filled with gutta-percha and AH Plus sealer using the continuous wave of condensation technique. At the fourteen-month reevaluation, the patient was asymptomatic, the tooth had remained functional, and radiographic and CBCT assessment showed significant osseous healing of the lesion. Successful non-surgical management of the present type II DI was achieved in the present case. The association of CBCT, dental operating microscope, XP-endo Finisher, NaOCl and MTA Repair HP were important for ensuring a predictable outcome.