A Distributed Control System is a concept of Network Control Systems whose applications range from industrial control systems to the control of large physical experiments such as the ALICE experiment at CERN. The design phase of the Distributed Control Systems implementation brings several challenges, such as predicting the throughput and response of the system in terms of data-flow. These parameters have a significant impact on the operation of the Distributed Control System, and it is necessary to consider them when determining the distribution of software/hardware resources within the system. This distribution is often determined experimentally, which may be a difficult, iterative process. This paper proposes a methodology for modeling Distributed Control Systems using a combination of Finite-State Automata and Petri nets, where the resulting model can be used to determine the system’s throughput and response before its final implementation. The proposed methodology is demonstrated and verified on two scenarios concerning the respective areas of ALICE detector control system and mobile robotics, using the MATLAB/Simulink implementation of created models. The methodology makes it possible to validate various distributions of resources without the need for changes to the physical system, and therefore to determine the appropriate structure of the Distributed Control System.