Maternal influenza infections pose a significant risk for neurodevelopmental disorders and have been linked to an increased incidence of autism and schizophrenia. While maternal immune activation is a well studied paradigm, most studies model only the acute stages due to use of synthetic viral mimetics. To investigate the impact of maternal influenza infection during pregnancy, we exposed pregnant mouse dams to influenza strains (dose of 1-3 LD50) with different virulence. Pregnant mice were exposed at different stages of gestation to understand whether cerebral cortical cell types showed differential vulnerability based on the time and length of exposure. We stained for distinct neural progenitor types to ascertain whether influenza exposure affected their renewal potential. We found a strain dependent impact on fetal and maternal health. Furthermore, we show that the gestational stage and length of exposure differentially affects neural progenitors. Specifically, infections carried out at embryonic day (E) 10 resulted in a greater change in progenitor renewal when studied at E13.5. We thus implemented single-cell transcriptomics at postnatal day 15 to identify cell types and extent of transcriptomic dysfunction due to gestational influenza exposure. Epidemiological studies have shown an important link between gestational influenza exposure and postnatal incidence of schizophrenia. Here we developed a mouse model to investigate which cell types are most vulnerable to such exposure. Our findings are hugely relevant for understanding the interplay between the immune system and the developing brain. Ultimately, our work may contribute in uncovering new therapeutic targets for neurodevelopmental disorders.