Aerobic exercise has been offered as a buffer against aging related decline in humans. Recently, evidence has indicated that chronological aging has been associated with decreases in measures of interhemispheric suppression during unimanual movements, but that such decreases may be mitigated by long-term aerobic fitness. The present research compared differences in measures of suppression of ipsilateral (right) primary motor cortex activity using functional magnetic resonance imaging (FMRI) and transcranial magnetic stimulation (TMS) during right hand finger movements. Participants groups were comprised of 14 sedentary older adults, 14 aerobically active older adults, and14 younger adults. All participants were right handed and reportedly healthy. Younger adults show the largest measures of ipsilateral primary motor cortex suppression as compared to older groups during both TMS (duration of ipsilateral silent period) and fMRI (magnitude of negative BOLD response). Aerobically active older adults show intermediate levels of interhemispheric suppression as compared to younger and sedentary older adults. Diffusion tensor imaging analysis did not reveal group differences associated with white matter density at motor crossing areas of the corpus callosum. These findings indicate that engagement in regular aerobic exercise may mitigate declines in suppression of the activity in ipsilateral primary motor cortex characteristic of sedentary aging.