This paper deals with the challenges involved in institutionalizing Monitoring and Evaluation practices within the scope of management of the Brazilian Unified Health System (SUS), based on the creation of a strategic agenda. This is structured around actions by the Federal Administration, from the perspective of defining the scope of the federative relationship. A summarized literature review is thus presented, placing into context the current SUS management process, which is based on the Pact for Health as well as theoretical and operational aspects inherent to monitoring and evaluation practices. The approach related to the strategic agenda highlights the creation of mechanisms that underpin the political and institutional decision, namely the creation of financial incentives and the development of technical mechanisms. These include organizational strategies for qualifying management teams and conducting studies and research and the dissemination of strategic information. These processes are based on the concept of providing for the management specificities in the different spheres of management based on a broad cooperation process involving teaching and research institutions and international organizations as well as the managers themselves.