The SARS-CoV-2 epidemic challenged universities and other academic institutions to rapidly adapt to urgent and life-threatening situations. It forced most institutions to shut down nearly every aspect of their research and educational enterprises. In doing so, university leaders were thrust into unchartered waters and forced them to make unprecedented decisions. Successes and failures along the way highlighted how the autonomous nature of the American academic research enterprise and skillsets normally required of university leaders were ill-suited to mounting an emergency response. Here, as faculty from medical centers in the United States, we draw lessons from these experiences and apply them as we plan for the next possible COVID-19-induced shutdown as well as other large-scale pandemics and emergencies at universities in the United States and throughout the world.