Alliances between the government and academic communities can be a key component of the public health response to an emergency such as the coronavirus disease 2019 (COVID-19) pandemic. The Governor of Puerto Rico designated the Puerto Rico Medical Task Force (MTF) COVID-19 to provide direct guidance and evaluation of the government response to the epidemic in Puerto Rico. Several work groups were formed within the MTF to create protocols and provide evidence-based recommendations on different public health aspects. The collaboration between the academia and the government enhanced the Puerto Rican public health response and contributed to the reduction seen in the contagion curve. Healthcare services and hospitals have not reached their maximum patient care capacity and the death toll has been controlled. Incorporating a national MTF with members of the academia into the government structure was beneficial during the COVID-19 response in Puerto Rico. A similar strategy could serve as a model for other states or territories and countries in similar scenarios.