The Brazilian Zika virus (ZIKVBR) outbreak has been linked to increased incidence of microcephaly; however, in vivo evidence for the effects of ZIKVBR on brain development is lacking. The authors show that pups born to SJL mice infected with ZIKVBR during pregnancy exhibit neuronal cell death and reduced cortical thickness as well as altered expression of autophagy- and cell death-related genes. ZIKVBR infection of human-derived neurospheres and cerebral organoids also impaired neural development and increased cell death. These models provide further evidence for the detrimental effects of ZIKVBR on cortical development and might enable the testing of strategies to counter the effects of the virus.