Cooperation between civilian and military forces, including the Japan Self-Defense Force (JSDF), enabled wide-ranging disaster relief after the Great East Japan Earthquake. Nevertheless, many preventable fatalities occurred, particularly related to an inability to treat chronic disease, indicating the need to plan for the provision of long-term medical aid after natural disasters in stricken areas and evacuation shelters. To assist in this effort, this report (1) provides an overview of the consequences of the medical response to the Great East Japan Earthquake, the largest natural disaster ever to hit Japan, focusing on the role and actions of the JSDF; (2) discusses the lessons learned regarding the provision of medical aid and management by the JSDF after this disaster, looking at the special challenges of meeting the needs of a rapidly aging population in a disaster situation; and (3) provides recommendations for the development of strategies for the long-term medical aid and support after natural disasters, especially with regard to the demographics of the Japanese population.