Ectopic mandibular third molar (EMTM) in the subcondylar region is a rare clinical condition, especially for a subtype confined between the mandibular foramen and condylar neck. The etiology is currently uncertain and the optimal management of this specific subtype remains not well defined. We reported a case of this specific subtype of EMTM that was minimally invasively extracted by endoscopy-guided intraoral surgery, planned preoperatively using three-dimensional (3D) imaging of cone beam computed tomography (CBCT), with no complications postoperatively caused by the routine surgery. We also reviewed nine relevant literature to expand the clinical features and therapeutic management of this specific subtype of EMTM. Etiologically, persistent cystic pressure may be a major cause of EMTM displaced into the subcondylar region. For extraction of this specific EMTM, the combination of 3D CBCT-based imaging and endoscopy-assisted intraoral minimally invasive surgery could be considered as the priority option for patients without facial fistula.