The COVID-19 pandemic generated a large volume of scientific productions with different quality levels. The speed with which knowledge was produced and shared worldwide imposed on health management the challenge of seeking ways to identify the best available evidence to support its decisions. In response to this challenge, the Department of Science and Technology of the Brazilian Ministry of Health started offering a service to produce and provide scientific knowledge addressing priority public health issues in the pandemic scenario. Drug treatments, non-pharmacological measures, testing, reinfection and immunological response, immunization, pathophysiology, post-COVID syndrome and adverse events are among the topics covered. In this article, we discuss the strengths and lessons learned, as well as the challenges and perspectives that present a real example of how to offer the best scientific evidence in a timely manner in order to assist the decision-making process during a public health emergency.