The subject of research is to determine the functional safety indicators of a fault-tolerant safety-critical system, namely, the minimal cut sets’ probability for a given duration of the system’s operation, using the state transition diagram (STD). The aim is to create a new method for analyzing the functional safety of a fault-tolerant safety-critical system. This method is based on the methodology of developing models of operational reliability behavior in the form of STD. This methodology provides a detailed representation of inoperable states and their relation with pre-failure (inoperable critical) states. The task is to propose a new classification for inoperable states of the STD to obtain all possible emergencies in the same space of inoperable states. This approach allows consideration the correlations between the failures, that it is impossible to use the fault trees. Since the space of inoperable states can reach hundreds and thousands of states, a method is proposed for their automated determination according to the classification. The state space method was used to conduct the validation of the method of functional safety analysis. The following results were obtained: the system of Chapman-Kolmogorov differential equations is formed in accordance with the STD and it provides the dependence of the functional safety indicator – the minimal cut sets’ probability as a function of the operational duration of the fault-tolerant safety-critical system. This dependence is called the emergency function. The method for determining the emergency function is based on the usage of the emergency mask. Note that the proposed model of operational reliability behavior in the form of STD provides the possibility to conduct both the functional safety and the reliability indicators. The value of the minimal cut sets’ probability for a given duration of operation is determined using the fault tree for the validation of the proposed method of functional safety analysis. The fault tree was built by Reliasoft BlockSim software. The obtained value coincides with the value of the minimal cut sets’ probability, which was defined by the emergency function for the same operational duration. Thus, the designer can comprehensively analyze the feasibility of introducing redundancy (structural, temporal, functional). Conclusions: the scientific novelty of the obtained results is the following: the new method for determining safe, critical and catastrophic states in the set of inoperable states is used in the methodology of the STD developing to obtain the stochastic model of operational reliability behavior of fault-tolerant safety-critical system. This technique ensures an automated defining of emergency function by using an improved structural-automatic model.