This report aims to demonstrate the phenotypic, radiological, and genetic features of encephalocraniocutaneous lipomatosis (ECCL), a rare neurocutaneous disorder characterized by a distinct triad of congenital skin lesions, ocular anomalies, and central nervous system (CNS) abnormalities. The mosaic nature of ECCL puts the radiologist in a unique position to facilitate its prompt diagnosis. In the patient reported here, pulmonic stenosis and facial dysmorphism initially raised the suspicion of Noonan syndrome, which was unsupported by genetic testing. Serial imaging revealed multiple intracranial lipomas and glioma along with a clinically evident nevus psiloliparus, prompting further genetic evaluation. This identified a novel de novo variant in FGFR1 (c.1685A > C, p.Glu562Ala). The variant appeared heterozygous in blood and cheek swab cells derived DNA, contrasting with the typical mosaic nature of variants in ECCL.