BackgroundDespite 20 years of democracy, South Africa still suffers from profound health inequalities. Gender roles and norms are associated with individuals’ vulnerability that lead to ill-health. For instance, gender inequality influences women’s access to health care and women’s agency to make health-related decisions. This paper explores gender-awareness and inclusivity in organisations that advocate for the right to health in South Africa, and analyses how this knowledge impacts their work?MethodsIn total, 10 in-depth interviews were conducted with members of The Learning Network for Health and Human Rights (LN), a network of universities and Civil Society Organisations (CSOs) which is explicitly committed to advancing the right to health, but not explicitly gendered in its orientation.ResultsThe results show that there is a discrepancy in knowledge around gender and gendered power relations between LN members. This discrepancy in understanding gendered power relations suggests that gender is ‘rendered invisible’ within the LN, which impacts the way the LN advocates for the right to health.ConclusionsEven organizations that work on health rights of women might be unaware of the possibility of gender invisibility within their organisational structures.Electronic supplementary materialThe online version of this article (10.1186/s12914-018-0172-4) contains supplementary material, which is available to authorized users.