This article discusses the difficulties of people whose sense of personal identity does not correspond with their assigned gender and who are recipients of welfare services, particularly of the Public Assistance (PA) system, in Japan. Semi-structured interview data from 3 cases and data of 36 visitors to an NGO in Tokyo supporting impoverished people were analyzed. We argue that the underlying cause for the difficulties experienced by transgender/gender-nonconforming people using the PA system is the cisgenderism built into the welfare system. Reviewing the recent developments in the PA system of Tokyo, focusing particularly on temporary accommodations, we reveal how cisgenderism works in the everyday operations of the welfare system. Analyzing the cases, we realized that the welfare office assigns the gender identity to PA applicants, which does not always correspond to their self-identity, based on which welfare services, including home-visit nursing and temporary accommodations, are provided. We also argue that temporary accommodations provided through PA are usually based on the binary conception of gender and gender segregation, and thus, combined with misgendering, fail to safely accommodate gender-nonconforming people who are homeless. In conclusion, we claim that within the recent developments in the PA system, transgender and gender-nonconforming people have been systematically excluded. We also propose that, to reduce the difficulties of gender-nonconforming people, merely enhancing welfare officers’ knowledge and understanding of sexual minorities is not enough; there is a greater need for the deconstruction of cisgenderism rooted in welfare systems.