Isolation rearing produces significant behavioral and neurochemical dysfunctions in rodents, which resemble the symptoms of schizophrenia. Clozapine, one of the atypical antipsychotics, is widely used in the treatment of schizophrenia patients and in experimental studies. In this study, male Sprague Dawley rats were randomly assigned to either group-reared or isolation-reared conditions during postnatal days (PNDs) 21-34. During PNDs 46-55, the rats were subjected to chronic clozapine (1.0 mg/kg for 10 days) or saline treatment. On PND 56, all rats underwent behavioral testing and then were sacrificed for biochemical testing. The results indicated that adolescent social isolation induced impairments in prepulse inhibition and reversal learning, and clozapine injection improved the prepulse inhibition disruption but not reversal learning ability. Furthermore, clozapine administration reversed the increased brain-derived neurotrophic factor (BDNF) mRNA level in the medial prefrontal cortex (mPFC) that was induced by adolescent isolation. However, clozapine decreased the BDNF mRNA level in the mPFC in group-reared rats. Together, our findings provide additional evidence that a low dose of chronic clozapine treatment could improve information filtering/sensorimotor gating and alterations in the BDNF mRNA level in the mPFC induced by adolescent social isolation.