Focal dermal hypoplasia (Goltz syndrome, Online Mendelian Inheritance in Man [OMIM] 305600) is a rare X-linked dominant congenital disorder involving defects of mesodermal- and ectodermal-derived structures. It is associated with mutations in the PORCN gene, a regulator of Wnt signaling proteins. The phenotype is highly variable, although all describe characteristic skin findings as a primary diagnostic feature. To date there are few case reports of focal dermal hypoplasia associated with central nervous system abnormalities. We report the second case of focal dermal hypoplasia associated with myelomenigocele, Arnold–Chiari malformation and hydrocephalus and the first in a male. Genetic testing identified a novel mosaic three base pair deletion within the PORCN gene (c.853_855delACG). This case highlights the importance of neurological evaluation in focal dermal hypoplasia and consideration of other syndromes more commonly associated with central nervous system abnormalities. In this report we summarize the literature on neurological manifestations in Goltz syndrome.