Abstract Infectious disease outbreaks represent potentially catastrophic threats to those affected by humanitarian crises. High transmissibility, crowded living conditions, widespread co-morbidities, and a lack of intensive care capacity may amplify the effects of the outbreak on already vulnerable populations and present humanitarian actors with intense ethical problems. We argue that there are significant and troubling gaps in ethical awareness at the level of humanitarian praxis. Though some ethical guidance does exist most of it is directed at public health experts and fails to speak to the day-to-day ethical challenges confronted by frontline humanitarians. In responding to infectious disease outbreaks humanitarian workers are likely to grapple with complex dilemmas opening the door to moral distress and burnout.