A 12-year-old Japanese boy was referred to our hospital for evaluation of a radiopaque area on the left side of the mandible. Radiographic and computed tomographic examinations revealed a radiopaque lesion located on the lingual side, along with permanent tooth eruption. Several small tooth-like structures were noted within the lesion and the mandibular left second premolar was inclined in a mesial direction. An odontoma was clinically diagnosed and surgical removal by an endoscopic intraoral approach under general anesthesia was planned. Reports of oral surgery using an endoscopic approach have been presented, though none for an odontoma. With the expectation that removal of the odontoma would improve dentition in this case, we planned future management. A minimally invasive surgical removal procedure by an endoscopic intraoral approach from the lingual side was performed and good early recovery was noted. The resected tumor consisted of several small tooth-like structures. Histopathological diagnosis was a compound odontoma. One-year follow-up findings showed that the post-surgical course was good.