MicroRNA124a (miR124a) has emerged recently as a key player for multiple neuropsychiatric disorders including depression, anxiety, alcoholism, and cocaine addiction. Although we have previously reported that miR124a and its target the brain-derived neutrophic factor (BDNF) play an important role in autism-like behaviors, the molecular and behavioral dysfunctions remain unknown. The aim of this study was to understand the effects of sustained decreases in miR124a and increases of BDNF in the dentate gyrus (DG) on neonatal isolation-induced anxiety-and autism like behaviors in rats. Here we report that lentiviral-mediated silencing of miR124a in the adult DG attenuated neonatal isolation-induced anxiety-like behavior in the elevated plus maze (EPM) and open-field (OF) tests. Also, miR124a silencing decreased autism-like phenotype in the marble burying test (MBT), self-grooming (SG), and social interaction tests. Pearson’s correlations demonstrated that high levels of BDNF, a direct target of miR124a, were negatively correlated with miR124a expression. Interestingly, viral-mediated BDNF overexpression in the DG also reversed the neonatal isolation-induced anxiety-and autism like phenotypes. Collectively, these findings suggest that miR124a, through its target BDNF, may influence neonatal isolation-induced anxiety-and autism like behaviors. In conclusion, these results do support the hypothesis that miR124a in discrete hippocampal areas contributes to anxiety- and autism-like behaviors and may be involved in the neuroadaptations underlying the development of autism spectrum disorders as a persistent and lasting condition, and therefore provide a clearer mechanistic framework for understanding the physiopathology of such psychiatric illnesses.