The effectiveness of repetitive transcranial magnetic stimulation on the post-stroke motor recovery is not apparent. To perform an accurate evaluation, we adjusted for critical factors that determine motor outcomes, including lesion location and the state of the corticospinal tract. We only included patients with cerebral infarct in the corona radiata and with corticospinal tract interruption, apparent on diffusion tensor tractography. We retrospectively enrolled 34 patients whose diffusion tensor tractography corticospinal tract was interrupted by a cerebral infarct. The corticospinal tract state of each patient was evaluated using diffusion tensor tractography. Of the 34 patients whose corticospinal tract was interrupted on diffusion tensor tractography, 12 patients underwent repetitive transcranial magnetic stimulation treatment at the early stage after cerebral infarct (repetitive transcranial magnetic stimulation group). In comparison, 22 patients did not receive repetitive transcranial magnetic stimulation treatment (non-repetitive transcranial magnetic stimulation group). High-frequency repetitive transcranial magnetic stimulation (10 Hz) was performed on the primary motor cortex of the affected hemisphere. At the six month evaluation after the onset of the infarct, motor function was measured in each patient. In both groups, compared to their states during the initial evaluation, significant improvement was found in all measurements of motor function. However, six months after onset, no significant differences between the two groups were found in these measurement scores. When a patient’s CST is interrupted, high-frequency repetitive transcranial magnetic stimulation treatment at the early stage after cerebral infarct might have no additional therapeutic effect on motor outcome. Qualified randomized controlled trials are needed to support our findings further.