Rabies virus (RABV) is known to cause a fatal infection in many mammalian species, yet its pathogenesis remains poorly understood. This study was performed to analyze the microRNA (miRNA) expression profiles in RABV-infected primary neurons of mice. A total of 53 miRNAs were found to be differentially expressed in RABV-infected samples compared with mock samples in a time-dependent manner. Among them, the expression of ten miRNAs was validated by real-time RT-PCR. Potential target genes of differentially expressed miRNAs were predicted by TargetScan. Further bioinformatics analysis indicated that these predicted targets were overrepresented in neuronal function-related Gene Ontology (GO) terms and biological pathways. The results of this study suggest that RABV may cause neuronal dysfunction by regulating cellular miRNA expression.