Background: Stroke is the leading cause of death and disability. Exercise produces neuroprotection by improving neuroplasticity. Exercise can induce exosome production. According to several studies, exosomes are involved in repairing brain function, but the relationship and mechanism of exercise, exosomes, and neuroprotection have not been elucidated. This study intends to explore the relationship and potential mechanism by observing the changes in the exosome level, infarct volume, neurological function and behavioral scores, synapses, and corticospinal tract (CST).Methods: Rats were randomly divided into four groups: a sham operation (SHAM) group, middle cerebral artery occlusion (MCAO) with sedentary intervention (SED-MCAO) group, MCAO with exercise intervention (EX-MCAO) group, and MCAO with exercise intervention and exosome injection (EX-MCAO-EXO) group. The exercise intervention was started 1 day after MCAO and lasted for 4 weeks. All rats were assessed using the modified neurological severity score (mNSS). The levels of exosomes in serum and brain, gait analysis, and magnetic resonance scan were performed 1 and 4 weeks after the intervention. After 4 weeks of intervention, the number of synapses, synaptophysin (Syn), and postsynaptic density protein 95(PSD-95) expression was detected.Results: After 4 weeks of intervention, (1) the EX-MCAO and EX-MCAO-EXO groups showed higher serum exosome (pEX−MCAO = 0.000, pEX−MCAO−EXO = 0.000) and brain exosome (pEX−MCAO = 0.001, pEX−MCAO−EXO = 0.000) levels than the SED-MCAO group, of which the EX-MCAO group had the highest serum exosome (p = 0.000) and the EX-MCAO-EXO group had the highest brain exosome (p = 0.03) levels. (2) The number of synapses in the EX-MCAO (p = 0.032) and EX-MCAO-EXO groups (p = 0.000) was significantly higher than that in the SED-MCAO group. The EX-MCAO-EXO group exhibited a greater number of synapses than the EX-MCAO (p = 0.000) group. (3) The synaptic plasticity-associated proteins were expressed significantly higher in the EX-MCAO (pSyn = 0.010, pPSD−95 = 0.044) and EX-MCAO-EXO (pSyn = 0.000, pPSD−95 = 0.000) groups than in the SED-MCAO group, and the EX-MCAO-EXO group (pSyn = 0.000, pPSD−95 = 0.046) had the highest expression. (4) Compared with the SED-MCAO group, the EX-MCAO group had significantly improved infarct volume ratio (p = 0.000), rFA value (p = 0.000), and rADC (p = 0.000). Compared with the EX-MCAO group, the EX-MCAO-EXO group had a significantly improved infarct volume ratio (p = 0.000), rFA value (p = 0.000), and rADC value (p = 0.001). (5) Compared with the SED-MCAO group, the EX-MCAO group (p = 0.001) and EX-MCAO-EXO group (p = 0.000) had significantly lower mNSS scores and improved gait. (6) The brain exosome levels were negatively correlated with the mNSS score, infarct volume ratio, and rADC value and positively correlated with the rFA value, Syn, and PSD-95 expression. The serum and brain exosome levels showed a positive correlation.Conclusions: Exercise intervention increases the serum exosome level in MCAO rats, which are recruited into the brain, leading to improved synaptic growth and CST integrity, a reduced infarct volume, and improved neurological function and gait.