It remains largely unknown how Zika virus (ZIKV) infection causes severe microcephaly in human newborns. We examined an Asian lineage ZIKV, SZ01, which similarly infected and demonstrated comparable growth arrest and apoptotic pathological changes in human neuroprogenitors (NPCs) from forebrain dorsal, forebrain ventral as well as hindbrain and spinal cord brain organoids derived from human pluripotent stem cells. Transcriptome profiling showed common overactivated antiviral response in all regional NPCs upon ZIKV infection. ZIKV infection directly activated a subset of IFN-stimulated genes (ISGs) in human NPCs, which depended on the presence of IRF3 and NF-κB rather than IFN production and secretion, highlighting a key role of IFN-independent acute antiviral pathway underlying ZIKV infection-caused neuropathy. Our findings therefore reveal that overactivated antiviral response is detrimental rather than protective in human NPCs, and the IFN-independent acute antiviral pathway may serve as a potential target to ameliorate ZIKV infection-triggered neuropathy.