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According to the modular hypothesis for the control of movement, muscles are recruited in synergies, which capture muscle coordination in space, time, or both. In the last two decades, muscle synergy analysis has become a well-established framework in the motor control field and for the characterization of motor impairments in neurological patients. Altered modular control during a locomotion task has been often proposed as a potential quantitative metric for characterizing pathological conditions. Therefore, the purpose of this systematic review is to analyze the recent literature that used a muscle synergy analysis of neurological patients’ locomotion as an indicator of motor rehabilitation therapy effectiveness, encompassing the key methodological elements to date. Searches for the relevant literature were made in Web of Science, PubMed, and Scopus. Most of the 15 full-text articles which were retrieved and included in this review identified an effect of the rehabilitation intervention on muscle synergies. However, the used experimental and methodological approaches varied across studies. Despite the scarcity of studies that investigated the effect of rehabilitation on muscle synergies, this review supports the utility of muscle synergies as a marker of the effectiveness of rehabilitative therapy and highlights the challenges and open issues that future works need to address to introduce the muscle synergies in the clinical practice and decisional process.