Analyses of gender-based violence during mass conflict have typically focused on violence committed against women. Violence perpetrated against men has only recently been examined as gender-based violence in its own right. Using narratives from 1,136 Darfuri refugees, we analyze patterns of gender-based violence perpetrated against men and boys during the genocide in Darfur. We examine how this violence emasculates men and boys through four mechanisms: homosexualization, feminization, genital harm, and sex-selective killing. In line with an interactionist approach, we demonstrate how genocidal violence is gendered and argue that perpetrators committing gender-based violence perform masculinity in accordance with hegemonic gender norms in Sudan. We also show how gender-based violence enacts, reinforces, and creates meaning on multiple levels in a matrix of mutually reinforcing processes that we term the gender-genocide nexus. By extending the gender–violence link to the context of mass atrocity, this study facilitates an understanding of the mechanisms through which gender inequalities can be reproduced and maintained in diverse situations and structures.