The paper distils results from a review of relevant literature and two gender analyses to highlight reasons for gender imbalances in senior roles in global health and ways to address them. Organizations, leadership, violence and discrimination, research and human resource management are all gendered. Supplementary materials from gender analyses in two African health organizations demonstrate how processes such as hiring, deployment and promotion, and interpersonal relations, are not ‘gender-neutral’ and that gendering processes shape privilege, status and opportunity in these health organizations. Organizational gender analysis, naming stereotypes, substantive equality principles, special measures and enabling conditions to dismantle gendered disadvantage can catalyze changes to improve women's ability to play senior global health roles in gendered organizations. Political strategies and synergies with autonomous feminist movements can increase women's full and effective participation and equal opportunities. The paper also presents organizational development actions to bring about more gender egalitarian global health organizations.