Transport is a fundamental part of logistics activities, which play a critical role in the development of society. The safety and the reliability of logistics transportation networks significantly affect those activities. Network vulnerability assessment has been applied in the passenger transport mode. However, the methodology to assess the vulnerability of logistics transportation networks should be developed differently from that of passenger or other transport modes because of the networks’ specific requirements for trip success. This paper proposes a methodology applicable in logistics transportation network vulnerability assessment. To evaluate the performance of logistics transportation networks, logistics value is included in the generalized cost of logistics transportation. Moreover, network vulnerability assessment is affected by the nature of the component degradation. Here, the performance of logistics transportation networks is evaluated in transportation facility degradation scenarios. A vulnerability scanning algorithm is applied in link and node degradation scenarios. To reduce computational demands, an efficient vulnerability scanning algorithm is applied to the simulation, and a computer program is developed to make this methodology feasible in large-scale networks. Finally, this methodology based on future highspeed railway planning is applied in a real logistics transport network in northern Japan. The research was undertaken to assist logistics managers, researchers, and transportation planners in defining and comprehending the basic views of the vulnerability of logistics transportation networks and their various applications.