During embryonic development, the cerebral cortex is equipped with excitatory projection and inhibitory interneurons that migrate in organized layers. Periventricular heterotopia (PH) is a rare and heterogeneous disorder in which a subpopulation of new-born projection neurons fails to initiate their radial migration to the cortex, ultimately resulting in bands or nodules of grey matter lining the lateral ventricles underneath a normal cortex. For many years, few genes had been identified that cause this disorder upon disruption, but recently it was shown that PH is genetically a very heterogeneous disease. Here, we study the neurodevelopmental role of endothelin converting enzyme 2 (ECE2), biallelic mutations in which have been identified in two patients with PH. Our results show that manipulation of ECE2 levels or activity in human cerebral organoids and in the developing mouse cortex leads to ectopic localization of neural progenitors and neurons. We uncover the role of ECE2 in neurogenesis and, mechanistically, we identify its involvement in generation and secretion of extracellular matrix and in protein phosphorylation. This strongly suggests ECE2 as a novel candidate gene for PH.