This study investigated the changes in motor evoked potential (MEP) amplitude and motor behavior index when paired associative stimulation (PAS), a conjoint stimulation of a peripheral nerve and the motor cortex, was applied in a rat stroke model. The PAS was applied to 19 rats and sham stimulation was applied to 15 rats. One part of PAS consisted of peripheral electrical stimulation of the soleus muscle and the other part was transcranial magnetic stimulation of the motor cortex. The stimulation was repeated for 30 min with a frequency of 0.05 Hz. Five sessions of PAS were applied over 5 consecutive days. The motor behavior index was higher in the PAS group than in the sham stimulation group at 7 d after ischemic brain injury. There was no lasting difference between the PAS animals and the sham stimulation group in MEP amplitude although MEP amplitude was increased immediately after PAS. MEP amplitude can be increased by the PAS paradigm in rats as well as in humans and PAS has potential therapeutic value for motor recovery after brain injury.