The effects of ethanol on neural function and development have been studied extensively, motivated in part by the addictive properties of alcohol and the neurodevelopmental deficits that arise in children with fetal alcohol spectrum disorder (FASD). Absent from this research area is a genetically tractable system to study the effects of early ethanol exposure on later neurodevelopmental and behavioral phenotypes. Here, we used embryos of the fruit fly, Drosophila melanogaster, as a model system to investigate the neuronal defects that arise after an early exposure to ethanol. We found several disruptions of neural development and morphology following a brief ethanol exposure during embryogenesis and subsequent changes in larval behavior. Altogether, this study establishes a new system to examine the effects of alcohol exposure in embryos and the potential to conduct large‐scale genetics screens to uncover novel factors that sensitize or protect neurons to the effects of alcohol.