This article examines the structural approach to health cooperation, focusing on its meaning as a method for promoting institutional policies to improve management models. We draw attention to the differences between this approach and the traditional disease-based approach, showing that the structural approach is centered on health systems, reinforces global governance, and embodies the Sustainable Development Goals (SDG), thus taking on a multi-sectoral dimension. This approach leverages the maximum potential of international cooperation by establishing structuring networks and promoting relations between partner countries through their national health institutions, schools of public health, and technical staff. By way of example, we show that this approach is applied in the Union of South American Nations (UNASUL, acronym in Portuguese) and Community of Portuguese-speaking Countries (CPLP, acronym in Portuguese), especially in Africa. Finally, we underline the importance of this approach for South-South relations, where it addresses the real necessities of partner countries, unlike North-South cooperation that is characterized by power asymmetries, especially within the economic and technical-scientific dimensions. Based on the experience developed in FIOCRUZ in the implementation of South-South international cooperation, the article analyzes the strategy of structuring cooperation in health, trying to highlight its meaning as a method of promoting institutional policies to refine the model of management. It draws attention to the difference with more traditional disease-oriented cooperation, while this approach focuses on the health system, reinforcing global governance and applying the Sustainable Development Goals (SDGs). Such an approach enhances cooperation with the establishment of structuring networks of institutions, including relations between countries within the scope of their National Institutes of Health and Schools of Public Health and Technical Personnel. The model is applied in the Union of South American Nations (UNASUR) and the Community of Portuguese Language Countries (CPLP), especially in Africa. Stresses the importance of this strategy in the South-South relationship, addressing the real needs of the associated countries as opposed to the asymmetries in the economic and scientific dimensions that are observed in the cooperation offered by developed countries.