Objective: Stroke results in limitation of active range of motion involving antagonist co-contraction. The analysis of brain-muscle connectivity can be used to deepen understanding of motor control alterations associated with the loss of motor function after stroke. This preliminary study aims to investigate the combined effects of botulinum toxin and rehabilitation on corticomuscular coherence to better understand the altered functional reorganization of the central-peripheral network. Methods: Kinematic, electromyographic and electroencephalographic data were recorded during twenty active elbow extensions in eleven chronic stroke patients and nine healthy control subjects. Active range of motion, antagonist co-contraction and corticomuscular coherence were calculated. Results: The initial increase in corticomuscular coherence in stroke patients was significantly reduced five weeks after the first botulinum toxin injection and twenty weeks away from the third injection, in both agonist and antagonist muscles, with moderate to large effect sizes, concomitantly with a decrease in antagonist co-contraction and an improvement in the active range of motion. Conclusions: This study highlights for the first time an effect of botulinum toxin injections combined with rehabilitation on corticomuscular coherence in stroke patients. Significance: Notwithstanding the relatively small sample, the results provide original evidence supporting treatment-induced effective functional reorganization of the central-peripheral network.