MicroRNAs (miRNAs) are very important regulators of biological processes such as development, cellular differentiation, and tumor generation. MiRNA microarray has been found to be a high throughput global analysis tool for detecting miRNA expression profiling, and miRNA expression profiling will facilitate the study of the biological function of miRNAs. In this report, we describe the miRNA expression level in rat cerebral cortex after traumatic brain injury using microarray method. We choose several time points post brain injury: 6 h, 24 h, 48 h and 72 h, respectively, to reveal differential expression of miRNAs in rat brain cortex compared with control groups. Our research revealed that 136 miRNAs were expressing at 6 h post injury, in which 13 miRNAs were more than 2-fold up-regulated, and 14 miRNAs were more than 2-fold down-regulated; 118 miRNAs were expressing at 24 h post injury, in which 4 miRNAs were more than 2-fold up-regulated, and 23 miRNAs were more than 2-fold down-regulated; 149 miRNAs were expressing at 48 h post injury, in which 16 miRNAs were more than 2-fold up-regulated, and 11 miRNAs were more than 2-fold down-regulated; and 203 miRNAs were expressing at 72 h post injury, in which 19 miRNAs were more than 2-fold up-regulated, and 5 miRNAs were more than 2-fold down-regulated. Furthermore, we revealed global up-regulation of miR-21 expression within all the four time points post injury. Finally, we utilized qRT-PCR methods to verify the microarray results. The qRT-PCR results indicated good consistency with the results of the microarray method. Our microarray based analysis of microRNA expression in rat cerebral cortex after traumatic brain injury has shown that some microRNA such as miR-21 could be involved in the intricate process of TBI course.