High consequence infectious diseases (such as Ebola virus or avian influenza) require specialist management with strict isolation to avoid spread to health-care staff and the wider community. These infections present various ethical and legal issues for children and young people. Specific challenges include the impact of isolation on the child and family (potentially without a child's consent), limitations to care due to staff safety considerations, and reduction of resources for other children (due to potential closure of paediatric intensive care unit beds). The complex decision making required in these scenarios needs timely ethical support. As planning for future pandemics accelerates, we suggest that the ethical and legal considerations involved in delivering care to affected children and their families need urgent consideration, and we have highlighted the important areas for focus to provide a route map for this important undertaking.