Glandular odontogenic cyst (GOC) is a rare odontogenic cyst with aggressive behavior. A 50-year-old Japanese man presented with pain and swelling of the mental region of the mandible. Panoramic radiography showed a clearly bordered radiolucent lesion extending from the alveolar to cortical bone of the mandible. The clinical diagnosis was an odontogenic tumor (e.g., ameloblastoma), and an incisional biopsy was performed. The histopathological diagnosis was GOC, and extirpation and tooth extraction were performed under general anesthesia. Because bone destruction is evident in patients with a huge GOC, it is important to differentiate these cysts from intraosseous mucoepidermoid carcinoma. Therefore, we analyzed the GOC for the presence of the CRTC1/3-MAML2fusion gene and found it to be negative. The patient had developed no recurrence of the GOC at the time of following.