To observe the clinical efficacy of repetitive peripheral magnetic stimulation (rPMS) combined with repetitive transcranial magnetic stimulation (rTMS) on post-stroke hemiplegic shoulder pain (HSP) and its impact on the somatosensory evoked potentials (SEPs) of the median nerve in the affected upper limb. Methods: Forty patients with HSP were randomly divided into an observation group (20 cases) and a control group (20 cases) using a random number table method. Both groups received conventional rehabilitation training. In addition, the control group was treated with high-frequency rTMS over the primary motor cortex of the affected side, while the observation group was treated with high-frequency rPMS targeting the painful trigger points of the rotator cuff muscles of the affected shoulder, combined with high-frequency rTMS over the primary motor cortex of the affected side. Treatments were administered once daily, five days a week, for four weeks. Before and after the intervention, subjects were assessed using the Short-Form McGill Pain Questionnaire (SF-MPQ), passive joint range of motion (PROM) of the pain-free hemiplegic shoulder, Neer shoulder function score, Modified Barthel Index (MBI), and the latency and amplitude of the N20 component of the median nerve SEP in the affected upper limb. Results: Before the intervention, there were no significant differences in baseline characteristics, SF-MPQ scores, PROM, Neer shoulder function scores, MBI, or the latency and amplitude of the N20 component of the median nerve SEP between the two groups (P>0.05). After the intervention, both groups showed a significant decrease in SF-MPQ scores compared to baseline (P<0.01), with a more pronounced decrease observed in the observation group than in the control group (P<0.05). Both groups also demonstrated significant improvements in PROM, Neer shoulder function scores, MBI, and N20 amplitude compared to baseline (P<0.05), with more significant improvements observed in the observation group than in the control group (P<0.05). After the intervention, the N20 latency in the observation group was significantly shorter than before the intervention (P<0.05), and the difference in N20 latency before and after the intervention was more pronounced in the observation group than in the control group (P<0.05). However, no significant difference in N20 latency was observed in the control group after the intervention (P>0.05). Conclusion: Peripheral-central combined magnetic stimulation is significantly effective in improving shoulder pain, shoulder joint function, and activities of daily living in patients with HSP. It also has a beneficial effect on the latency and amplitude of the N20 component of the median nerve SEP, with superior outcomes compared to rTMS treatment alone.