Chronic stress causes various detrimental effects including cognitive and affective dysfunctions. Given the recent findings emphasizing the importance of information processing between the prefrontal cortex (PFC) and limbic structures on cognitive and affective functions, impairments of these functions caused by chronic stress may be associated with stress-induced adaptive and maladaptive responses in limbic structure–PFC interaction. In this study we have shown that chronic stress disrupts limbic structure–PFC interaction by modulating N-methyl-D-aspartate (NMDA) receptor expression in the PFC. We found that chronic stress decreased expression of NR1, NR2A and NR2B subunits of NMDA receptors in the PFC but not in the motor cortex. However, the reduction in NR2B subunits of NMDA receptors was larger in the dorsal part than the ventral part of PFC. In agreement with this observation, administration of the NMDA antagonist that was more selective for NMDA receptors containing NR2B subunits induced alterations of synchronous local field potentials between the PFC and limbic structures, synaptic plasticity induction in the limbic structure–PFC pathway, and spike firing of PFC neurons that were similar to those observed in the dorsal PFC of rats exposed to chronic stress. In contrast, administration of the NMDA antagonist that was not subunit-selective resulted in electrophysiological alterations resembling to those observed in the ventral PFC of rats exposed to chronic stress. These results suggest that chronic stress disrupts NMDA receptor-dependent limbic structure–PFC information processing.