DNA double-strand breaks (DSBs) frequently occur in rapidly dividing cells such as proliferating progenitors during central nervous system development. If they cannot be repaired, these lesions will cause cell death. The non-homologous end joining (NHEJ) DNA repair pathway is the only pathway available to repair DSBs in post-mitotic neurons. The non-homologous end joining factor 1 (Nhej1) protein is a key component of the NHEJ pathway. Nhej1 interacts with Xrcc4 and Lig4 to repair DSBs. Loss of function of Xrcc4 or Lig4 is embryonic lethal in the mouse while the loss of Nhej1 is not. Surprisingly, the brains of Nhej1-deficient mice appear to be normal although NHEJ1 deficiency in humans causes severe neurological dysfunction and microcephaly. Here, we studied the consequences of Nhej1 dysfunction for the development of the cerebral cortex using in utero electroporation of inactivating small hairpin RNAs (shRNAs) in the developing rat brain. We found that decreasing Nhej1 expression during neuronal migration phases causes severe neuronal migration defects visualized at embryonic stages by an accumulation of heterotopic neurons in the intermediate zone. Knocked-down cells die by 7 days after birth and the brain regions where RNA interference was achieved are structurally abnormal, suffering from a reduction of the width of the external cortical layers. These results indicate that the Nhej1 protein is necessary for proper rat cortical development. Neurons unable to properly repair DNA DSBs are unable to reach their final destination during the development and undergo apoptosis, leading to an abnormal cortical development.