Although the South African apartheid regime was first and foremost a race-based project, it was also a gendered project. The regime’s dystopian vision to entrench the systematic oppression of non-white people, particularly black people, was rooted in an ideological commitment not just to white supremacy, but to white male supremacy. This paper unpacks the gendered experiences of apartheid and outlines potential avenues to facilitate a more intersectional approach to justice and accountability efforts. Part I traces the patriarchal vision underpinning the South African apartheid regime—and the distinctly gendered dimensions of apartheid’s operationalization and legacy. Adopting a comparative approach, Part II turns to Israel’s ongoing perpetration of apartheid in the occupied Palestinian territories and the gendered axes of its infrastructure. Part III considers the challenge with existing justice efforts in adequately reflecting how patriarchy and the entrenchment of socially constructed gender roles permeate apartheid systems, including in relation to the emerging norm of gender apartheid. Drawing from other areas of international criminal law and international human rights law, Part IV explores how justice and accountability efforts can better reflect the intersecting harms experienced by victims and survivors of apartheid, including by recognizing multiple and concurrent axes of discrimination and oppression in the commission of atrocity crimes.