Morning glory syndrome is a congenital anomaly of the optic disc in which the disc is enlarged and excavated, with white glial tissue in the center. A case is presented of morning glory syndrome associated with sphenoid encephalocele, median cleft lip, and agenesis of the corpus callosum. A 22-day-old boy was referred to the Wakayama Medical College Hospital for management of dyspnea due to a soft-tissue mass in the oral cavity. Magnetic resonance imaging revealed a mass extending through a bone defect in the sphenoid region and into the oral cavity. Surgical repair was attempted through a bifrontal craniotomy. A bone defect was identified in the sphenoid plate, through which the arachnoid membrane was connected to the oral cavity. Both optic nerves were elongated and adhered to the encephalocele. The wall of the meningocele was compressed digitally through the oral cavity and sutured to the dura mater of the bone defect. The operative findings suggest that a basal encephalocele protruding from a bone defect in the sphenoid plate may disturb the normal development of the optic nerve.