We evaluated the hand motor function of a right hemiparetic patient with schizencephaly using a combination of fMRI, transcranial magnetic stimulation, and diffusion tensor tractography (DTT). Only the unaffected (right) primary sensori-motor cortex was found to be activated during either affected (right) or unaffected hand movements. Evoked motor potentials with similar characteristics were obtained from both abductor pollicis brevis muscles simultaneously when stimulating the unaffected motor cortex. Moreover, a tract presumed to be a corticospinal tract was observed in the unaffected hemisphere by DTT, however, no tract was observed in the affected hemisphere. Our results indicate that the ipsilateral corticospinal tract extended from the unaffected (right) motor cortex to both hands. This finding may reflect functional reorganization of motor function in a patient with congenital brain disorder.