It is common following stroke to focus early rehabilitation efforts on developing compensatory use of the less-affected body side. Here we used a rat model of focal cortical infarct to examine how motor skill acquisition with the less-affected (“intact”) forelimb influences sensorimotor function of the infarct-impaired forelimb and neural activity in peri-infarct cortex. Rats proficient in skilled reaching with one forelimb were given focal ischemic lesions in the contralateral sensorimotor cortex (SMC). Recovery in this forelimb was tested following a period of reach training focused on the intact forelimb or control procedures. Quantitative measures of the cumulatively expressed transcription factor, FosB/ΔFosB, were used to assay intact forelimb training effects on neuronal activity in remaining SMC of the infarcted hemisphere. Intact forelimb training worsened behavioral recovery in the impaired forelimb following unilateral focal ischemia. Furthermore, it decreased neuronal FosB/ΔFosB expression in layer II/III of peri-infarct SMC. These effects were not found in sham-operated rats trained sequentially with both forelimbs or in animals receiving bilateral forelimb training after unilateral infarcts. Thus, focused use of the intact forelimb has detrimental effects on recovery of impaired forelimb function following a focal ischemic injury and this is linked to reduced neuronal activation in remaining cortex. These results suggest that peri-infarct cortex becomes vulnerable to early post-stroke experience with the less-affected forelimb and that this experience may drive neural plasticity here in a direction that is maladaptive for functional outcome.