Basal encephalocele is a rare craniofacial anomaly. In the present paper we report a 10-year-old boy presented with cleft palate, congenital nystagmus, and hypertelorism. During preoperative evaluation for cleft palate repair, a pulsatile mass was detected in the pharynx. Magnetic resonance imaging showed sphenoethmoidal type of basal encephalocele and agenesis of corpus callosum. Neurosurgical consultation was performed for further evaluation and management.