Rabies is a deadly neurotrophic virus, which causes tens of thousands of deaths every year, and many of its victims are children under the age of 15. Rabies specifically infects and spreads in the host nervous system. However, the pathogenesis of Rabies virus in neurons is not fully understood. Rabies infection is clinically manifested as the furious form in 80% of the cases, where the virus silently spreads through the neuronal axons without any damage. However, in other 20% of infections, Rabies virus damages the axons of peripheral neurons, resulting in paralysis. We studied the pathogenesis of different laboratory-adapted and wildtype strains of Rabies virus, using cultured primary mouse neurons from the central and peripheral nervous system. In this comprehensive study, we have identified a novel host defense mechanism in response to specific strains of Rabies infection, which results in the self-destruction of neuronal axons. Using pharmacological inhibitors and neurons from a gene knockout mouse model, we have now identified the complete signaling pathway behind this axonal self-destruct mechanism in neurons. Furthermore, by developing a new in-vitro microfluidic model for synaptically connected neurons, we show that this axonal self-destruction reduces spreading of Rabies virus between connected neurons. These results implicate that neurons activate axonal self-destruction as a defense mechanism to break infected axons and impede the spread of the virus in the nervous system. However, in the majority of infections, Rabies virus is able to evade this neuronal defense mechanism resulting in the furious form of the disease. Therefore, we have identified a novel type of innate immune response executed by neurons, which could be the key determinant of clinical outcome in Rabies infections. These findings significantly improve our understanding of Rabies virus pathogenesis in neurons and identify novel therapeutic targets for neurotrophic viral infections.