Previous studies have suggested that brain-derived neurotrophic factor (BDNF) and trkB both have a role in plasticity following brain insults and exercise increases BDNF and trkB mRNA levels in the normal brain. We attempted to determine whether treadmill exercise improves motor function following experimental cerebral ischemia, and whether motor outcome is associated with BDNF and trkB expression. We subjected adult male Sprague-Dawley rats to a permanent ischemia, followed by either 12 days of treadmill exercise or non-exercise. In the exercise group, improvements in the motor behavior index were found and BDNF and trkB proteins in contralateral hemisphere were increased. This study suggests that after permanent brain ischemia, exercise improves motor performance and elevates BDNF and trkB proteins in the contralateral hemisphere.