The purpose of this study was to compare the effects of rTMS and FES on the recovery of upper limb function in stroke patients and to provide basic data that can be used in clinical practice. The design of this study was a randomized, controlled, double-blind study. Sixteen subjects were randomly assigned to the rTMS group (n=8) and the FES group (n=8). The subjects did not know their group until the end of the study. The subjects received rTMS and FES respectively before the traditional rehabilitation training, which was performed once daily (30 min), 5 times a week for 6 weeks, for a total of 30 sessions. To evaluate the excitability of the motor cortex of stroke patients, motor evoked potentials (latency and stimulus intensity) were measured. In addition, the manual function test (MFT) was used to evaluate upper limb function. there was no significant difference in the general characteristics of the subjects (p>0.05). In the comparison between the two groups, there was no significant difference in the Latency, Amplitude, Box and Block Test after the intervention. In the comparison within each group, there was a significant difference in the MFT test after the intervention in the rTMS group (p<0.05), and there was no significant difference in all variables in the FES group (p>0.05). rTMS is effective in improving upper limb function in stroke patients, and it suggests that it is an effective intervention method for upper limb function rehabilitation that noninvasively stimulates the central nervous system.