This paper deals with the problem of managing the risks of complex systems under targeted attacks. It is usually solved by using Defender–Attacker models or similar ones. However, such models do not consider the influence of the defending system structure on the expected attack outcome. Our goal was to study how the structure of an abstract system affects its integral risk. To achieve this, we considered a situation where the Defender knows the structure of the expected attack and can arrange the elements to achieve a minimum of integral risk. In this paper, we consider a particular case of a simple chain attack structure. We generalized the concept of a local risk function to account for structural effects and found an ordering criterion that ensures the optimal placement of the defending system’s elements inside a given simple chain structure. The obtained result is the first step to formulate the principles of optimally placing system elements within an arbitrarily complex network. Knowledge of these principles, in turn, will allow solving the problems of optimal allocation of resources to minimize the risks of a complex system, considering its structure.