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Zika virus is an arbovirus that has reemerged in recent years as a global health concern. A member of the Flavivirus genus, Zika virus is closely related to other major human pathogens such as dengue virus and West Nile virus, but each of these viruses exhibit varied clinical pathologies. While Zika virus was first discovered in 1947, it was not until the outbreaks across the Pacific and Americas from 2013 onward that Zika virus’ unique neuropathies were revealed. Of particular concern was the potential for vertical transmission and teratogenic effects in infected pregnant women, prompting the World Health Organization to declare Zika virus a public health crisis of global concern in 2016. Even with a growing knowledge of Zika virus’ adverse fetal outcomes and the characterization of congenital Zika syndrome, much research is still needed to understand the cellular and molecular mechanisms underlying these potentially devastating infection consequences. Given this need, we therefore established a cerebral organoid system to model Zika virus exposure throughout fetal brain development. When exposed to Zika virus, organoids, which recapitulated features of brain development in the first trimester, exhibited microcephaly-like restrictions in maturation. This included an overall reduction of organoid growth, enlargement of the ventricle-like structures, and increased cell death in organoids exposed to both the prototypical and modern epidemic strains of Zika virus. In older organoids resembling the fetal brain structure of the second trimester, Zika virus preferentially infected neural progenitor cells as compared to neurons, and also infected several other early brain cell types, demonstrating the potential cellular affects underlying Zika virus-induced microcephaly. We next utilized a neuroglia-derived cell line highly permissive to Zika virus infection to find Zika virus host factors in neural cells. We identified the host protein, AXL, as an important factor for Zika virus infection, but observed a difference in the requirement of AXL for the infection of Zika and dengue virus. Chimeras of Zika and dengue virus revealed that the structural proteins displayed on the virion surface were a major determinant of AXL-dependent viral infection. Lastly, we investigated the molecular mechanisms contributing to AXL-dependent infection and found that suppression of the IFN response as mediated by AXL was minimally involved in AXL-dependent Zika virus infection, in contrast to dengue virus, suggesting that different aspects of AXL signaling may facilitate Zika and dengue infection in neuroglia. Our data provide a model system for evaluating Zika virus exposure during fetal brain development. We show that Zika virus infects both neural progenitor cells and neuroglia, cell types which are present at different stages of cerebral cortex development. Our work highlights the importance of AXL in Zika virus infection of neuroglia and the differential requirement of AXL for Zika and dengue virus infection. Collectively, these findings contribute toward dissecting the mechanism by which Zika virus utilizes AXL for viral entry and infection, which may be important for understanding Zika virus pathogenesis as AXL is expressed on many of the cell types infected by the virus in vivo.