Military aeronautical projects in Brazil need to demonstrate compliance with mission-related requirements during the certification phase. When designing a system, the System Safety Analysis (SSA) is an essential part of the engineering activities related to initial airworthiness. Such an analysis requires a process to determine whether the system is secure enough and to identify an acceptable balance between security, cost, and military capability. The concern with military capacity is sometimes equal to or greater than the aspects related to the security of the operation, as they aim at a specific and innovative objective. Ensuring the safety of systems and products used in fulfilling their missions rests with the competent authorities, who need to conduct a reasoned assessment of the risk of specific operations. To fill this gap, developing a guide that serves as a support tool for risk assessment decisions in a given operation is necessary. In this article, the authors draw on their experience in certifying military aeronautical products to (1) briefly review the concept of risk acceptance applied to aeronautical design; (2) present the risk analysis method applied in military aeronautical projects in Brazil; (3) present a method that substantiates the acceptance of residual risk for military aeronautical projects in Brazil; and (4) Finally, this work presents the use of the method that substantiates the acceptance of residual risk through an application in the operation of uncrewed aircraft.