•We investigated how MS affects the mPFC linked to social behavior using rodents.•MS decreased the number of inhibitory neurons and synapses in the mPFC.•MS impaired the social behavior deeply related to the mPFC.•MS attenuated cell activity in the mPFC during social recognition task.•Social deficits by MS is likely to be caused by E/I imbalance in the mPFC. Aversive environmental conditions during early life are known to cause long-lasting social deficits, similar to those observed in patients with neurodevelopmental disorders. However, the mechanism of how early life stress can cause social deficits is not well understood. To clarify how being in an aversive environment during development affects sociability, we conducted various analyses focusing on the excitatory and inhibitory (E/I) balance in the medial prefrontal cortex (mPFC) and how it is related to social deficits, with young adult male rats that had been exposed to maternal separation (MS). In our MS procedure, part of the pups were separated from each dam for 3 h, twice a day, during postnatal days 2–20, and then were used for each analysis at 9 weeks old. We identified that MS mainly reduced pre- and post-synaptic protein expression of inhibitory neurons in the mPFC, and that decreased the number of GAD67-positive interneurons and inhibitory synapses in the mPFC. Furthermore, MS impaired social behavior related to social recognition, which is closely linked to the mPFC, in the three-chamber sociability and social novelty test (3-CST). With relation to this social deficit, immunohistological analysis revealed that c-fos-positive cells in the mPFC of rats exposed to MS decreased during the 3-CST. Considering that inhibitory neurons in the mPFC play a role in synchronizing neural activation for information processing, our findings demonstrate that MS-induced E/I imbalance associated with cell activity in the mPFC leads to deficits in social recognition.