Medical school asylum clinics are complex organizations that blend medical and legal expertise with service to assist individuals seeking refuge from human rights violations. The balance of power shared by the students and faculty who lead these clinics varies widely across institutions, usually in an inverse reciprocal relationship. The Weill Cornell Center for Human Rights will observe its 10th anniversary in 2020 and is notable for espousing maximal student autonomy in the organization’s governance with minimal faculty control or administration participation. This level of autonomy requires that, in addition to successfully running the organization, student leaders must adeptly manage logistical, administrative, and ethical challenges without compromising the trust and confidence of the medical college and larger university. This article describes a series of difficult decisions involving policy, conflict resolution, and resource management made expeditiously by the student leadership. Ethical dilemmas, operational challenges, and the difficulties imposed by an unexpected global catastrophe—the COVID-19 pandemic—are presented alongside detailed descriptions of how these issues were deliberated and resolved by the student leadership.