On one hand, no one can deny the importance of the information system in today’s industrial and logistic activities. The progress in IT tools and systems allowed to process real-time data giving the opportunity to enhance considerably the management of production and transportation operations. On the other hand, supply chain digitalization is a sensitive process that can generate increased risks for the companies’ activities. Therefore, such risks should be identified and managed. In this study, we follow Failure Mode, Effects, and Criticality Analysis (FMECA) approach to assess the risk linked to the information system of supply chains. We also present the methodology and choices adopted to apply this study in an aeronautical supply chain case.