Background: Neurological diseases and traumas are major factors that may reduce motor functionality. Functional electrical stimulation is a technique that helps regain motor function, assisting patients in daily life activities and in rehabilitation practices. In this study, we evaluated the efficacy of a treatment based on whole-body Adaptive Functional Electrical Stimulation Kinesitherapy (AFESK™) with the use of muscle synergies, a well-established method for evaluation of motor coordination. The evaluation is performed on retrospectively gathered data of neurological patients executing whole-body movements before and after AFESK-based treatments. Methods: Twenty-four chronic neurologic patients and 9 healthy subjects were recruited in this study. The patient group was further subdivided in 3 subgroups: hemiplegic, tetraplegic and paraplegic. All patients underwent two acquisition sessions: before treatment and after a FES based rehabilitation treatment at the VIKTOR Physio Lab. Patients followed whole-body exercise protocols tailored to their needs. The control group of healthy subjects performed all movements in a single session and provided reference data for evaluating patients’ performance. sEMG was recorded on relevant muscles and muscle synergies were extracted for each patient’s EMG data and then compared to the ones extracted from the healthy volunteers. To evaluate the effect of the treatment, the motricity index was measured and patients’ extracted synergies were compared to the control group before and after treatment. Results: After the treatment, patients’ motricity index increased for many of the screened body segments. Muscle synergies were more similar to those of healthy people. Globally, the normalized synergy similarity in respect to the control group was 0.50 before the treatment and 0.60 after (p < 0.001), with improvements for each subgroup of patients. Conclusions: AFESK treatment induced favorable changes in muscle activation patterns in chronic neurologic patients, partially restoring muscular patterns similar to healthy people. The evaluation of the synergic relationships of muscle activity when performing test exercises allows to assess the results of rehabilitation measures in patients with impaired locomotor functions.