In this paper, the focus is upon daily school practices in Junior Secondary Schools in Ghana and Botswana. The data from 12 ethnographic case studies have been used to explore how the institution of schooling is gendered. The analysis focuses predominantly on the informal practices of the hidden curriculum through a theoretical perspective that highlights these institutional processes as significant to the production of gender/sexual identities. Remarkable similarities in the pervasive and inequitable gender/sexual practices within schools across country contexts are discussed in three key areas: school management and duties, gender space and gender violence. These discussions of everyday school life illustrate the ways in which both normative institutional practices and human agency produce and regulate gender/sexual identities. This micro-level analysis provides important substantive and methodological insights into what goes on inside schools and into the contexts and experiences of schooling that are significant to policy discourses of gender, education and development.