Malformations of cortical development (MCD) are important causes of chronic epilepsy. MCD encompass many varied disorders with diverse clinical manifestations. Schizencephaly, one of the MCD, is known to be complicated by various types of epilepsy, most of which are intractable. We treated a 28-year-old man with epilepsy, characterised by unprovoked generalised tonic–clonic seizures accompanied by MCD. Brain MRI detected multiple malformations including septum pellucidum defect, partial corpus callosum defect, schizencephaly, right hippocampal atrophy, cerebellar atrophy and cerebellum atrophy. 99m Tc-ethylcysteinate dimer single photon emission CT showed decreased cerebral blood flow (CBF), and the morphology of CBF defects overlapped with the anomalous findings on MRI. The clinical outcome of the patient was good despite his severe brain malformations. Although the reason of this discrepancy is unclear, the outcomes of social function and epileptic seizures may be relatively good despite severe MCD in some patients.