While physical rehabilitation facilitates some recovery, it is uncommon for patients to recover completely from stroke. Cell based therapies derived from stem cells have produced promising results in enhancing recovery in pre-clinical studies, but the mechanism is not yet completely understood. We previously evaluated human umbilical tissue-derived cells (hUTC) in our non-human primate model of cortical injury, limited to the hand area of primary motor cortex. hUTC treatment, injected intravenously 24 hours after injury, resulted in significantly greater recovery of fine motor function compared to treatment with vehicle. Based on these striking findings, in the current study, we investigated the hypothesis that hUTC treatment leads to functional recovery through reducing cytotoxic responses and enhancing neurorestorative processes following cortical injury. Brain sections were assessed using histological techniques to quantify perilesional oxidative damage, hemosiderin accumulation, microglial activation, Betz cell number, synaptic density, and astrocytic complexity. Brain sections outside of the primary area of injury were also assessed for microglial activation in white matter pathways, cell activation through c-Fos in premotor cortices, and neurogenesis in neurogenic niches. Finally, blood samples from throughout the recovery period and CSF samples from 16 weeks after injury were analyzed for BDNF levels. In the perilesional area, hUTC treatment was associated with lower oxidative damage and hemosiderin accumulation, but not with a difference in microglial activation. hUTC also resulted in a trend toward higher astrocyte complexity and synaptic density in the lesion area, but no difference in ipsilesional Betz cell number. Further, hUTC treatment led to more microglia in white matter pathways, higher c-Fos activation in ventral premotor cortex, and a trend toward higher neurogenesis in the hippocampus. Finally, BDNF levels were higher in blood with hUTC treatment one week after injury, but there was no change beyond one week in blood serum or in CSF, when compared with vehicle. Taken together, these results suggest that hUTC treatment modulates immune responses, limits perilesional damage and cell death, enables neuroplasticity and reorganization, and enhances acute neurotrophic factor secretion. While many cell therapies are currently undergoing clinical trials, this study advances our understanding of the mechanism of cell based therapies.