This work aimed to study mylohyoid motor-evoked potentials (MHMEPs) and examined if it is related to chronic stroke dysphagia. Conduction time (CT) and amplitudes of the right and left MHMEPs in response to focal cortical magnetic stimulations over affected and unaffected hemispheres were recorded in 16 stroke patients with aspiration (n = 9) or residue (n = 7) and compared with eight control patients. In control group, MHMEPs were present on ipsilateral and contralateral sides after stimulation of both hemispheres and permitted to determine a dominant hemisphere. In stroke patients, after stimulation of the affected hemisphere, ipsilateral MEPs had a longer CT and lower amplitudes in patients with aspiration compared with patients with residue or control patients (P < 0.05). Contralateral CT was not different between the three groups, but amplitudes were lower in patients with residue and aspiration than in control patients (P < 0.01). In the unaffected hemisphere, MHMEPs were present, and not different between the three groups for the ipsilateral side and amplitudes were decreased in contralateral side in patients with residue. In conclusion, MHMEP alterations of the affected hemisphere related to chronic stroke dysphagia severity and were closed to normal in the unaffected hemisphere.