Background Glenohumeral subluxation (GHS) is common in patients with acute hemiplegia caused by stroke. GHS and upper limb function are closely related. Objective Using musculoskeletal ultrasonography (MSUS) to objectively evaluate the efficacy of functional magnetic stimulation (FMS) in the treatment of GHS in acute hemiplegic patients after stroke. Methods The study used prospective case control study. Stroke patients with GHS were recruited and assigned to control group and FMS group. Control group received electrode stimulation at the supraspinatus and deltoid muscles of the hemiplegic side, while FMS group was stimulated at the same locations. Before and after treatment, the distances of the acromion-greater tuberosity (AGT), acromion-lesser tuberosity (ALT), acromiohumeral distance (AHD), supraspinatus thickness (SST), and deltoid muscle thickness (DMT) in patients' bilateral shoulder joint were measured by MSUS, respectively. Meanwhile, Fugl-Meyer Assessment (FMA) was used to evaluate the improvement of upper limb function. Results 30 patients were recruited. After FMS treatment, there was a significant decrease in the difference value between ipsilateral side and contralateral side of AGT [t = 8.595, P < 0.01], ALT [t = 11.435, P < 0.01], AHD [t = 8.375, P < 0.01], SST [t = 15.394, P < 0.01], and DMT [t = 24.935, P < 0.01], and FMA score increased [t = −13.315, P < 0.01]. Compared with control group, FMS group decreased more significantly in the difference value between ipsilateral side and contralateral side of AGT [t = 2.161, P < 0.05], ALT [t = 3.332, P < 0.01], AHD [t = 8.768, P < 0.01], SST [t = 6.244, P < 0.01], and the DMT [t = 3.238, P < 0.01], and FMA score increased more significantly in FMS group [t = 7.194, P < 0.01]. Conclusion The study preliminarily shows that the MSUS can objectively and dynamically evaluate the treatment effect of GHS in hemiplegic patients. Meanwhile, compared with control group, the FMS is more effective and has fewer side effects, and the long-term effect of FMS is worth further study. This trial is registered with ChiCTR1800015352.