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Objective To evaluate a novel multi-channel functional electrical stimulation (FES) rehabilitation method based on the evaluation of patient-specific walking dysfunction. Methods This study investigated a novel multi-channel FES-based rehabilitation method that analysed the patient’s muscle synergy and walking posture. A patient-specific FES profile was produced in the pre-evaluation stage by comparing the muscle synergy and walking posture of the patient with those of healthy control subjects. During the rehabilitation phase, this profile was used to determine an appropriate FES pulse width and amplitude for stimulating the patient’s muscles as they walked across a flat surface. Results Two stroke patients with hemiplegic symptoms participated in a clinical evaluation of the proposed method involving a 4-week course of rehabilitation. An evaluation of the rehabilitation results based on a comparison of the pre- and post-rehabilitation muscle synergy and walking posture revealed that the rehabilitation enhanced the muscle synergy similarity between the patients and healthy control subjects and their quantitative walking performance, as measured by a 10-m walk test and walking speed, by up to 23.38% and 30.00%, respectively. Conclusion These results indicated that the proposed rehabilitation method improved walking ability by improving muscle coordination and adequately supporting weakened muscles in stroke patients.