Recent advances in neurophysiological brain network analysis have demonstrated novel potential for diagnosis and prognosis of disorders of consciousness. While most progress has been achieved on the population-sample level, time-economic and easy-to-apply personalized solutions are missing. This prospective controlled study combined EEG recordings, basal stimulation, and daily behavioral assessment as applied routinely during complex early rehabilitation treatment. We investigated global characteristics of EEG-derived evolving functional brain networks during the repeated (3–6 weeks apart) evaluation of brain dynamics at rest as well as during and after multisensory stimulation in ten patients who were diagnosed with an unresponsive wakefulness syndrome (UWS). The age-corrected average clustering coefficient C* allowed to discriminate between individual patients at first (three patients) and second assessment (all patients). Clinically, only two patients changed from UWS to minimally conscious state. Of note, most patients presented with significant changes of C* due to stimulations, along with treatment, and with an increasing temporal distance to injury. These changes tended towards the levels of nine healthy controls. Our approach allowed to monitor both, short-term effects of individual therapy sessions and possibly long-term recovery. Future studies will need to assess its full potential for disease monitoring and control of individualized treatment decisions.