Objective: To investigate the effects of the low-frequency repetitive transcranial magnetic stimulation (LF-rTMS) combined with acupuncture in the treatment of shoulder joint pain on patients after stroke. Methods: Sixty patients suffering from shoulder joint pain were selected to conduct the research and were randomly divided into three groups, an acupuncture group, a rTMS group and a combined therapy group, patients from the acupuncture group were given acupuncture with conventional rehabilitation. Specifically, the rTMS group in the contralateral hemisphere upper limb motor area were given 1 Hz rTMS, where M1 area (upper extremity motor function of cerebral motor cortex) of contralateral hemisphere is simulated, the combined therapy group were given 1 Hz rTMS on the basis of the treatment. The scores of simple Fugl-Meyer Assessment (FMA) and Visual Analogue Scale (VAS) before the treatment, 4 weeks after the treatment were used to evaluate the upper limb movement function recovery. Results: The upper limb FMA score and VAS score in the rTMS group were 4.55±0.83, 7.90±0.79 and 6.90±0.91, 4.45±0.51 respectively; in the acupuncture group patients the scores were 4.50±0.76, 11.60±1.27 and 6.80±0.95, 3.20±0.52 respectively; and in the combined therapy group were 4.70±0.80, 18.0±1.45 and 6.85±0.99, 1.75±0.45 respectively; the FMA scores of the groups increased after treatment, meanwhile the scores of VAS reduced, and the difference was statistically significant. Comparison between groups, the scores of FMA and VAS of the combined group and the acupuncture group were superior to the group of rTMS, and the scores of combined groups were superior to the groups of acupuncture, and the difference was statistically significant. Conclusion: Acupuncture with 1 Hz transcranial magnetic stimulation can significantly reduce the shoulder joint pain after stroke.