We modulated neural excitability in the human motor cortex to investigate behavioral effects for both hands. In a previous study, we showed that decreasing excitability in the dominant motor cortex led to a decline in performance for the contralateral hand and an improvement for the ipsilateral hand; increasing excitability produced the opposite effects. Research suggests that the ipsilateral effects were mediated by interhemispheric inhibition. Physiological evidence points to an asymmetry in interhemispheric inhibition between the primary motor cortices, with stronger inhibitory projections coming from the dominant motor cortex. In the present study, we examined whether there is a hemispheric asymmetry in the effects on performance when modulating excitability in the motor cortex. Anodal and cathodal transcranial direct current stimulation were applied to the motor cortex of 17 participants, targeting the non-dominant hemisphere on one day and the dominant hemisphere on another day, along with one sham session. Participants performed a finger-sequence coordination task with each hand before and after stimulation. The dependent variable was calculated as the percentage of change in the number of correct keystrokes. We found that the effects of transcranial direct current stimulation depended upon which hemisphere was stimulated; modulating excitability in the dominant motor cortex significantly affected performance for the contralateral and ipsilateral hands, whereas modulating excitability in the non-dominant motor cortex only had a significant impact for the contralateral hand. These results provide evidence for a hemispheric asymmetry in the ipsilateral effects of modulating excitability in the motor cortex and may be important for clinical research on motor recovery.