Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impaired social communication and repetitive/restricted behaviors. Folate is essential for normal fetal development and growth. Our previous study has described that prenatal folate deficiency (FD) mice have exhibited ASD-like decreased sociability. Also, they have showed increase in convulsant-induced seizure susceptibility and decrease in anxiety-like behavior. In this study, we examined the changes in the relative expression of N-methyl-D-aspartate (NMDA)-type glutamate receptor, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate receptor, postsynaptic density protein 95 (PSD-95), and GABA-synthesizing enzymes (GAD65/67) in the prefrontal cortex (PFC). We found that the expression of NMDA receptor subunit 2b, AMPA receptor 1, PSD-95, and GAD65/67 were significantly decreased in FD mice compared with control mice. These results may suggest that decrease in both of excitatory and inhibitory synapse-related proteins in the PFC could have effects on behavioral impairment of FD mice.