People with Fetal Alcohol Spectrum Disorders (FASDs) may present deficits in executive functions. The fronto-striatal circuit is a critical component of the fronto-basal ganglia pathway that plays an important role in executive processes. We used resting-state functional MRI to assess the effects of prenatal alcohol exposure on the functional interaction within the fronto-striatal circuit in a rat FASD model. Male alcohol-exposed rats, but not females, showed reduced fronto-striatal connectivity. Further exploratory analysis revealed a reduction in cortico-striatal connectivity in female alcohol-exposed rats, suggesting that prenatal alcohol exposure has sex dependent effects on executive and sensory processing functions.