Stroke induces a loss of neural function, but it triggers a complex amount of mechanisms to compensate the associated functional impairment. The present study aims to increase our understanding on the functional reshape of the motor system observed in chronic stroke patients during the preparation and the execution of movements. A cohort of fourteen chronic stroke patients with a mild-to-moderate hemiparesis and fourteen matched healthy controls were included in this study. Participants were asked to perform a bimanual reaction time task synchronizing alternated responses to the presentation of a visual cue. We used Laplacian-transformed EEG activity (LT-EEG) recorded at the locations Cz and C3/C4 to study the response-locked components associated to the motor system activity during the performance of this task. Behaviorally, patients showed larger variable errors in synchronizing the frequency of execution of responses to the ISI and slower responses compared to controls. LT-EEG analysis showed that while control participants increased their SMA activity during the preparation of all responses, patients only showed this activity during their first response of the sequence. More interestingly, patients showed a clear increment of the LT-EEG activity associated to SMA short after responses compared to control participants. Finally, patients showed a hand-dependent inhibitory activity over motor areas ipsilateral to the response hand. Overall, our findings reveal drastic differences in the temporal dynamics of the LT-EEG components associated to the activity over motor and premotor cortices in chronic stroke patients compared to matched control participants during alternated hand responses.