Background: Ischemic stroke results in high morbidity and mortality, and mitochondrial dysfunctions play a crucial role in the associated pathological process. Although exogenous mitochondria were used to treat ischemic stroke-induced brain injury, its effects and related mechanisms remain poorly understood, as is the fate of exogenous mitochondria during/after internalization by targeted cells. Methods: The mitochondrial morphology, membrane potential, DNA copy number, mitochondrial stress, metabolic characteristics and tumorigenicity of mNSCs and Neuro-2a cells were evaluated. Hypoxia/reoxygenation-induced cell injury was performed, and after mitochondrial supplementation, the viability, ROS levels, apoptosis and transcriptomic changes were assessed by CCK-8, DCHF-DA probes, flow cytometry, WB and next-generation sequencing analyses. The fate of exogenous mitochondria was further explored using fluorescent dyes and fusion protein analyses during/after internalization by targeted cells. Rat tMCAO models were generated using a suture-occluded method, and at 24 h after mitochondrial transplantation, behavioral changes and brain infarction areas were estimated by multiple score scales and TTC staining, respectively. Results: In this research, we found that mitochondria of Neuro-2a cells had some notable differences compared to that of mNSCs on mitochondrial membrane potential, DNA copy number, stress response and metabolic characteristics, but their shapes were similar and were both no tumorigenicity. Exogenous mitochondrial treatment could increase the cellular viability in an oxygen-dependent pattern, decrease the cellular ROS generation and apoptosis, and alter the transcriptomic characteristics after subjected to hypoxia/reoxygenation in vitro. Selective component recombination might occur during/after internalization of exogenous mitochondria by host cells and was observed with mitochondrial fluorescent dyes and engineered fusion protein. Moreover, mitochondrial transplantation could significantly improve tMCAO-induced rat neurobehavioral deficiency and brain infarction. Conclusions: The results of our present study offer a promising therapeutic strategy for ischemia/reperfusion-induced brain injury and provide preliminary insights regarding the effects and fate of exogenous mitochondria during/after being internalized into host cells.