Abstract Background Multiobjective decision-making processes present a high degree of complexity in their solution, and tools such as multicriteria decision analysis appear as a way to facilitate the decision-makers’ solution and ensure that the decision is made cohesively and efficiently. In the public health sector, decisions are even more delicate because they work not only with the direct influence of human needs, but also with limited financial resources. An important point for the emergency care units is the triage system, which consists of a pre-evaluation of the patients, classifying them according to the degree of life risk. Through triage, the patient can be attended more quickly and efficiently, streamlining the whole process. Thus, the present research endeavored to determine the most appropriate triage protocol for emergency healthcare units in Natal-RN city in Brazil and may help others less advanced countries to determine the most appropriate triage protocol for emergency healthcare. Methods In this study, we used the multicriteria analysis method known as FITradeoff. In addition, interviews and structured questionnaires applied with nurses, specialists and directors. Results Based on the questionnaires and preferences presented by the decision-makers, the Spanish Triage System was the most suitable protocol for the emergency care units, which presented with high ease of use and implementation. Conclusions This study reached its main objective, which was to determine the most appropriate triage protocol. In addition, it was observed the possibility of new research, such as the development of a specific protocol for this emergency care units and the creation of an application software for this new protocol.