Prenatal exposure to Zika virus (ZIKV) can result in microencephaly and congenital Zika syndrome but why some brain cells and structures are initially spared by the virus is unknown. Here, a novel murine model of ZIKV infection incorporating in utero electroporation with cell type specific promotors was used to identify the time course of ZIKV infection and to determine which neural precursor cells are initially infected or spared. In vivo time course studies revealed early presence of ZIKV in apical radial glial cells (aRGCs) while infection of basal intermediate progenitor cells climbed after three days of virus exposure. ZIKV-exposed fetal brains exhibited microencephaly as early as 1 day post injection, caused by apoptosis and reduced proliferation, and this change in brain size persisted until birth regardless of developmental age at infection. During infection, 60% of aRGC basal fibers were perturbed while 40% retained normal morphology, indicating that aRGCs are not uniformly vulnerable to ZIKV infection. To evaluate this heterogeneous vulnerability, we generated cell type-specific fate mapping plasmid probes using a previously published single cell RNA-Seq dataset on the E15.5 mouse neocortical wall. The results indicate that one class of aRGC preferentially expresses the putative ZIKV entry receptor AXL, and that these cells are more vulnerable to ZIKV infection than the other aRGC subtypes with low AXL expression. Together, these data highlight important temporal and cellular details of ZIKV fetal brain infection and may be important for prevention strategies and for management of congenital Zika syndrome.