The central nervous system simplifies motor control by sending motor commands activating groups of muscles, known as synergies. Physiological locomotion can be described as a coordinated recruitment of four to five muscle synergies. The first studies on muscle synergies in patients affected by neurological diseases were on stroke survivors. They showed that synergies can be used as biomarkers for motor impairment as they vary in patients with respect to healthy people. Likewise, muscle synergy analysis has been applied to developmental diseases (DD). The need for a comprehensive view of the present findings is crucial for comparing results achieved so far and promote future directions in the field. In the present review, we screened three scientific databases and selected thirty-six papers investigating muscle synergies extracted from locomotion in children affected by DD. Thirty-one articles investigate how cerebral palsy (CP) influences motor control, the currently exploited method in studying motor control in CP and finally the effects of treatments in these patients in terms of synergies and biomechanics; two articles investigate how muscle synergies vary in Duchenne muscular dystrophy (DMD), and three other articles assess other developmental pathologies, such as chronic and acute neuropathic pain. For CP, most of the studies demonstrate that the number of synergies is lower and that the synergy composition varies in the affected children with respect to normal controls. Still, the predictability of treatment’s effects and the etiology of muscle synergy variation are open questions, as it has been reported that treatments minimally modify synergies, even if they improve biomechanics. The application of different algorithms in extracting synergies might bring about more subtle differences. Considering DMD, no correlation was found between non-neural muscle weakness and muscle modules’ variation, while in chronic pain a decreased number of synergies was observed as a possible consequence of plastic adaptations. Even if the potential of the synergistic approach for clinical and rehabilitation practices is recognized, there is not full consensus on protocols nor widely accepted guidelines for the systematic clinical adoption of the method in DD. We critically commented on the current findings, on the methodological issues and the relative open points, and on the clinical impact of muscle synergies in neurodevelopmental diseases to fill the gap for applying the method in clinical practice.