Clear cell odontogenic carcinoma (CCOC), a rare tumor in the head and neck region, displays comparable properties with other tumors clinically and pathologically. In consequence, an incorrect diagnosis may be established. A 51-year-old male patient who was admitted to the Department of Oral and Maxillofacial Surgery at Pusan National University Dental Hospital was initially diagnosed with ameloblastoma via incisional biopsy. However, the excised mass of the patient was observed to manifest histopathological characteristics of ameloblastic carcinoma. The lesion was ultimately diagnosed as clear cell odontogenic carcinoma by the Department of Oral Pathology of Pusan National Dental University. Therefore, segmental mandibulectomy and bilateral neck dissection were performed, followed by reconstruction with fibula free flap and reconstruction plate. Concomitant chemotherapy radiotherapy was not necessary. The patient has been followed up, and no recurrence has occurred 6 months after surgery.