Infarcts from proximal middle cerebral artery (MCA) stroke can produce impairments in motor function, particularly finger movements in humans and digit flexion in rats. In rats, the extent of neural damage may be limited to basal ganglia structures or may also include portions of the frontal and parietal cortex in severe cases. Although the primary motor cortex (M1) is anatomically spared in proximal MCA occlusion, its functional integrity is suspect because even a small subcortical infarct can damage neural circuits linking M1 with basal ganglia, brainstem, and spinal cord. This motivated the present study to investigate the neurophysiological integrity of M1 after transient proximal MCA occlusion. Rats, preoperatively trained and non-preoperatively trained to reach for food, received extensive reach training/testing with the contralateral-to-lesion paw for several weeks after MCA occlusion. The forelimb movement representations were assayed from the ipsilateral-to-lesion M1 with intracortical microstimulation approximately 10 weeks after MCA occlusion. Digit flexion was impaired during food grasping in rats with relatively small subcortical infarcts and was completely abolished in rats that sustained at least moderate subcortical damage. Corresponding forelimb movement representations ranged from abnormally small to absent. The results suggest that ischemia in subcortical territories of the MCA does not spare the neurophysiological properties of M1 despite its apparent anatomical intactness, probably because of damage sustained to its descending fibers. Thus, M1 dysfunction contributes to the impairments that ensue from proximal MCA occlusion, even when the infarct is limited to subcortical regions.