Political challenges to prioritizing gender in global health organisations Background Many global health organisations have adopted formal strategies to integrate gender in their programming. In practice, few prioritise the issue. Institutions with considerable global power therefore largely overlook fundamental drivers of adverse health outcomes: gender inequality and harmful gender norms. We analyse the factors shaping attention to gender in organisations involved in global health governance. Methods Drawing on scholarship from the fields of organisational behavior and management, sociology, international relations and the policy process, we undertook a thematic analysis of peer-reviewed scholarship and organisational documents. We also conducted 20 semi-structured interviews over Skype with individuals working at the cross-section of gender and health. Results In seeking to reform the policies and practices of global health organisations, gender proponents confront patriarchal organisational cultures, hostile political environments and an issue that is difficult to address as it requires upsetting existing power structures. Proponents also face three linked challenges internal to their own networks. First, there is little cohesion among champions themselves, as they are fragmented into multiple networks. Second, proponents differ on the nature of the problem and solutions, including whether reducing gender inequality or addressing harmful gender norms is the primary goal, the role of men in gender initiatives, which health issues to prioritise, and even the value of proponent cohesion. Third, there are disagreements among proponents on how to convey the problem. Some advance an instrumental case, while others believe that it should be portrayed as a human rights issue and using any other argument undermines that fundamental justification. Conclusions Prospects for building more gender-responsive global health organisations will depend in part on the ability of proponents to address these disagreements and develop strategies for negotiating difficult organisational cultures and political environments.