A basal encephalocele is a rare congenital malformation involving a cranial bone defect and cystic-like herniation through the defect. Moyamoya is a rare cerebrovascular disease of unclear etiology involving occlusion of the distal internal carotids and formation of collateral vascular networks. Both diseases have been correlated with optic disc anomalies, hypopituitarism, and midfacial defects. We present a case of a 2-year-old boy with a midline facial cleft who underwent surgical correction of a basal encephalocele. His moyamoya disease may have contributed to a vascular complication. There is growing evidence indicating an overlap in disease profiles for these two rare diseases. In addition, molecular evidence indicates elevated levels of fibroblast growth factor and transforming growth factor in both diseases, suggesting common molecular pathways.