Traumatic brain injury (TBI) causes a neurological impairment of the central nervous system that may induce severe motor deficits. In this study, human cranial bone-derived mesenchymal stem cells (hcMSCs) were transplanted into a mouse TBI model, and the effects of differences in exercise frequency were examined as a rehabilitation approach to improve motor function after cell transplantation. Twenty-four hours after TBI induction, phosphate-buffered saline or hcMSCs were intravenously injected into mice that were divided into a non-exercise group, a low-frequency exercise group (LF Ex), and a high-frequency exercise group (HF Ex). Beam walking tests and rotarod tests were performed over time to assess motor function. Injured brain tissues were collected for mRNA and protein expression analysis on days 8 and 35 after TBI induction. On days 28 and 35 after TBI induction, significant associations were found between hcMSC transplantation (T) and exercise factors. Notably, the T + HF Ex group exhibited a significant improvement in motor function compared with the other groups. Moreover, we found that the mRNA and protein expression levels of growth associated protein 43 (GAP-43), hepatocyte growth factor (HGF), and nerve growth factor (NGF) were significantly higher in the T + HF Ex group than in other groups. Increased expression of GAP-43 enhances synaptic regeneration and promotes functional recovery. High expression of NGF accelerates neural differentiation, and HGF ensures the efficacy of hcMSCs. These data suggest that hcMSC transplantation combined with high-frequency exercise is a promising option for TBI treatment.