Scholarship on socially-engaged religion in Japan and research on the non-profit sector in that country tend to be mutually disregarding. This article attempts to fill the gap between the scholarship on socially-engaged religion and that on the non-profit sector. It first outlines the ways in which legal categories of civil society organisations in Japan hinder the identification of religious organisations with the rest of the non-profit sector. Second, it places organised religion within Japan’s broader non-profit sector. Finally, the article examines the connections between religious and civil society organisations in other non-profit sectors. The cases suggest that organised religion is involved in some form or other in all of the major sectors of the broader non-profit sector but that their participation varies both by sector and religion.