This case study contrasted two subjects with stroke who received 6-Hz primed low-frequency repetitive transcranial magnetic stimulation (rTMS) to the contralesional primary motor area (M1) to disinhibit ipsilesional M1. Functional magnetic resonance imaging (fMRI) showed that the intervention disrupted cortical activation at contralesional M1. Subject 1 showed decreased intracortical inhibition and increased intracortical facilitation following intervention during paired-pulse TMS testing of ipsilesional M1. Subject 2, whose precentral knob was totally obliterated and who did not show an ipsilesional motor evoked potential at pretest, still did not show any at posttest; however, her fMRI did show a large increase in peri-infarct zone cortical activation. Behavioral results were mixed, indicating the need for accompanying behavioral training to capitalize on the brain organization changes induced with rTMS.