The Virtual Brain (TVB) is a novel modeling platform to simulate whole-brain dynamics starting from individual structural and functional connectivity. In this work, we performed TVB simulations in neurodegenerative diseases (i.e. Alzheimer’s disease, Frontotemporal Dementia, and Amyotrophic Lateral Sclerosis) providing a unique description of the excitatory/inhibitory balance at single-subject level. TVB-derived biophysical parameters were different among clinical phenotypes, presented an association with neuropsychological domains and improved discriminative power between clinical conditions. Overall, this work suggests a novel TVB-based approach for future personalized diagnosis and therapy in neurodegenerative diseases, providing a subject-specific description of excitation/inhibition profiles.