Traumatic brain injury (TBI) is an insult to the brain that results in impairments of cognitive and physical functioning. Both of human research and animal studies demonstrate that spontaneous exercise can facilitate neuronal plasticity and improve cognitive function in normal or TBI rodent models. However, the possible mechanisms underlying are still not well known. We postulated that spontaneous running wheel (RW) altered microRNA (miRNA) expressions in hippocampus of mice following TBI, which might be associated with the improvement in cognitive functions. In the present study, acquisition of spatial learning and memory retention was assessed by using the Morris water maze (MWM) test on days 15 post RW exercise. Then, microarray analyses in miRNA files were employed, and the expressional changes of miRNAs in the hippocampus of mice were detected. The results showed that spontaneous RW exercise (i) recovered the hippocampus-related cognitive deficits induced by TBI, (ii) altered hippocampal expressions of miRNAs in both of sham and TBI mice, and (iii) miR-21 or miR-34a was associated with the recovery process. The present results indicated that an epigenetic mechanism might be involved in voluntary exercise-induced cognitive improvement of mice that suffered from TBI.