A 47-year-old male with a left middle cerebral artery embolism due to a left atrial myxoma was admitted to our hospital for severe right hemiparesis (Brunnstrom Recovery Stage I in all parts) and total aphasia. On day 29, the tumor was extracted but he developed complete AV block as a complication after surgery. Rehabilitation was delayed for a long time and the severe hemiparesis remained unchanged. He required assistance even when taking a sitting position on the bed, but muscle tonus appeared on the right lower limb. Beginning on day 59, before pacemaker implantation, we applied high-frequency repetitive transcranial magnetic stimulation to his bilateral lower limb motor areas for 5 consecutive days. As a result, paresis in the right lower limb improved to Brunnstrom Recovery Stage III and he could walk between parallel bars. On day 67, a pacemaker was implanted. On day 88, he could walk independently with a cane on discharge from our hospital, although the upper limb and hand paresis remained severe. Although there has been no report on the use of transcranial magnetic stimulation on the lower limb motor area except in the chronic stage, our experience suggests that this type of intervention can be effective in the recovery stage as well. Since transcranial magnetic stimulation is not feasible after pacemaker implantation, careful assessment is necessary for determining the precise indication for this treatment.