A case of congenital lipodystrophy complicated by complex-partial epilepsy is reported in a nine-year-old girl. The peculiarity of this rare case is represented by partial complex epilepsy with diffuse electroencephalographic alterations represented by a continuous seizure-like pattern that persisted unmodified despite the successful antiepileptic treatment. Although the etiopathology of lipodystrophy is, at present, still elusive, we hypothesize that the primitive dysfunction of lipidic metabolism plays a critical role in both determining central nervous system (CNS) alterations and the findings that characterized this extremely rare disease.