The community quarantines against COVID-19 in the Philippines, which began in March 2020, are considered some of the most stringent pandemic restrictions in the world. They have severely affected the Japanese community in the country, with the population of Japanese expatriates in the Philippines decreasing from 17,753 in 2019 to 15,728 in 2021, as per residency reports to the Embassy of Japan in the Philippines. During this period, what happened to the Japanese community and how were the Japanese nationals affected under the hard lockdowns? This is the research question that this paper attempts to find answers to. This simple question has hardly been answered in the existing studies in the field of social sciences, which renders this descriptive study valuable. Also, this study sheds light on the vulnerability of an overseas Japanese community through the description of their problems that emerged during the crisis, thereby providing fundamental information for the examination of policy challenges that both the Japanese and Philippine governments face. The scope of this study is limited to the Japanese community in the Philippines. This paper describes the primary difficulties that Japanese nationals have confronted during the pandemic in qualitative and quantitative ways. In particular, this paper focuses on four kinds of difficulties: (1) the inability of Japanese students to return to Japan or to re-enter the Philippines after temporarily leaving, (2) the hardships of new employees at Japanese-affiliated companies in the Philippines in entering the country, (3) the financial difficulties and bankruptcy of Japanese-affiliated enterprises, and (4) the lack of access to Japanese-approved COVID-19 vaccines for Japanese residents.