The air traffic environment is a complex system that involves several players. Between the air navigation service provider (ANPS) and the final client, many different organizations act with different purposes but are strongly interfaced. Changes and modifications in terms of technology, predefined process, or personnel are constantly needed, requiring coordination among the stakeholders. However, due to the high level of interaction between the players, any change in a complex system like the air traffic environment requires risk management. This paper demonstrates the suitability and advantages of the System-Theoretic Accident Model and Processes/Systems-Theoretic Process Analysis (STAMP/STPA) method to be applied to the risk assessment of an operational air traffic modification. The method, which had never been used on an air traffic problem in Brazil before, was applied considering the implementation of segregated simultaneous operation at the Guarulhos International Airport. The results were proven to be effective in terms of deriving useful safety requirements. From such demonstration, STAMP/STPA can be considered as a feasible alternative to the brainstorming method currently applied for risk assessment and generation of safety requirements regarding modifications in the structure of the air traffic services (ATS) in Brazil.