The present case report describes the endodontic treatment of a type III B dens invaginatus (DI) in a three-rooted mandibular second molar since the invagination invades the root and extends apically. Clinical and cone-beam computed tomography examination of the mandibular second molar showed a broadened coronal morphology, DI, a third root, periapical radiolucency, and compression of a distal root canal by the invagination, which developed an atypical semilunar shape. The tooth was diagnosed with pulpal necrosis, symptomatic apical, and peri-invagination periodontitis. Consequently, three-dimensional virtual reconstruction was conducted to improve anatomical interpretation and case planning and accelerate the intraoperative phase by reducing operator stress and minimizing intraoperative variables. The present case report aims to raise awareness of the existence of DI on the mandibular second molar.