Based on experience during the Great East Japan Earthquake, this article examines the efficiency and high-security requirements of Japan’s pharmaceutical supply chain and its response pattern in an emergency. Ensuring supply chain security requires an enormous amount of investment, sacrifices, and improvement in efficiency. The practical measures being implemented need to maintain a strict balance between supply chain security and efficiency. To assess the supply chain security needs of the pharmaceuticals, interviews were conducted with Japan’s pharmaceutical supply chain players. Although faced with some difficulties, the supply chain functioned effectively during the sudden change in demand following the 2011 quake. The distribution centers are located mainly in the three major metropolitan areas unevenly, but dispersing inventories are maintained at all the branch offices outside the area of specific lead time. However, this article has found that the changes in the pharmaceutical supply chain could lead to a low level of security. The national or local governments might be required to provide public assistance for the management. Additional measures might be needed if differences between municipalities in the extent of the measures result in substantial regional disparities in access to pharmaceuticals. Users and suppliers need to continue risk communication about how much money they should invest in secure supply chain. Geographical studies are required to contribute to the spatial arrangement of the pharmaceutical supply chain that considers both moderation of the medical insurance system’s finances and the supply chain’s function as a social infrastructure.