Aplasia cutis congenita (ACC; MIM 107600) is a congenital skin disorder that manifests as localized absence of skin. Here we report a case of familial ACC and mega-cisterna magna. A female neonate was born with skin defects on the scalp. Brain magnetic resonance imaging demonstrated retrocerebellar space widening suggesting mega-cisterna magna. Her father also had a skin defect on the scalp at birth, and brain computed tomography of the father showed a cystic lesion over the right occipital lobe, similar to the patient's brain imaging. Karyotype 46,XX, t(6;18)(q23.2;q11.2) was identified on G-banded karyotype analysis of the patient and her father, after which whole exome sequencing was carried out, but this was thought to be a coincidental finding. This indicates that ACC may be associated with brain anomaly, although it is very rare.