Diaphragmatic eventration is a rare congenital anomaly characterized by the replacement of diaphragmatic muscle with fibroelastic tissue, leading to diaphragm elevation and functional impairment. While it can occur in isolation, it is sometimes associated with congenital syndromes, including septo-optic dysplasia (SOD). This report presents a case of diaphragmatic eventration in a neonate with Fryns syndrome presenting with cleft palate and SOD, highlighting diagnostic challenges.