Dens invaginatus is a well-known malformation of teeth, which probably results from an invagination of enamel organ into dental papilla during tooth development. The endodontic treatment of invaginated teeth may be challenging due to difficulties in accessing the root canals and also due to complex variations of internal morphology. This article presents the endodontic management and follow-up in a rare case of right mandibular second premolar with Oehlers' type III dens invaginatus. The result of cold pulp testing was positive for this tooth but it was associated to a sinus tract and periapical lesion. Herein, it is described the root canal therapy of this tooth combined with periapical surgery, emphasizing the importance of proper diagnosis and planning by using cone beam computed tomography (CBCT). This case report presents the proper periapical healing 6 months after the combination of nonsurgical and surgical treatments. It also shows that CBCT is an important auxiliary examination to avoid errors in diagnosis and subsequent treatment of dental anomalies.