Previous studies have suggested that impairment occurs in the lower motor neuron (LMN) pathway after stroke, but more research remains to be supported. In this study, we tested the hypotheses: (1) both motor cortex and peripheral nerve pathways have decreased excitability and structural damage after stroke; (2) parameters of transcranial magnetic stimulation motor evoked potentials (TMS-MEP) can be used as predictors of motor function and stroke prognosis. We studied five male cynomolgus monkeys with ischaemic stroke. TMS-MEP, cranial MRI, behavioural assessment, neurological scales and pathology were applied. Elevated resting motor threshold (RMT) (p<0.05), decreased TMS-MEP amplitudes (p<0.05) and negative RMT lateralisation were detected in both the affected motor cortex (AMC) and the paretic side median nerve (PMN) at 2 weeks poststroke. Disturbed structure and loose arrangement of myelin sheaths were observed in the PMN through H&E staining and LFB staining at 12 weeks poststroke. The primate Rankin Scale (used for assess the stroke prognosis) scores at 2-12 weeks after middle cerebral artery occlusion were [1, (1; 3)], [1, (1;2)], [1, (1; 1.5)] and [1, (1; 1.5)], respectively. The RMT and RMT lateralisation (AMC) were predictors of stroke prognosis, and the RMT lateralisation of PMN and latency of AMC were predictors of motor impairment. Both upper motor neuron (UMN) and LMN pathway excitability is reduced after stroke, and structural damage in median nerve 12 weeks after stroke occur. In addition, RMT and RMT lateralisation are predictors of stroke prognosis and motor impairment.