Although studies have demonstrated that several specific brain lesions are related to the severity of functional outcomes, the effects of specific brain lesions are not yet clear. This study investigated the effects of hemorrhagic stroke lesions on motor recovery. Eleven subjects with hemorrhagic stroke were assessed. Using the Fugl-Meyer Assessment and functional ambulation category, clinical motor and sensory impairments were tested four times in total: initially within 2 weeks and 1, 3, and 6 months after the onset of stroke. Brain lesions and size were evaluated using MRIcron, SPM8, and Talairach Daemon software. Trunk control, motor function in the lower limbs, and sensory function improved significantly within 3 months, after which the change was no longer significant. Upper limb function and gait were unchanged within 1 month but improved significantly 3 months after onset and continued to improve for 6 months. Involvement of the anterior putamen, internal capsule, thalamus, periventricular white matter, and premotor cortex was related to poor upper limb recovery in patients with hemorrhagic stroke. These results should be useful for planning rehabilitation strategies and understanding the prognosis of hemorrhagic stroke.