This article explores the ongoing ‘gender blindness’ of global health governance in public health emergencies, with specific focus on the Ebola and Zika virus outbreaks. By beginning with an overview on the gendered inequalities evident in global health, the authors outline the disproportionate mortality of women in childbirth in developing countries as opposed to a developed. Similarly, in the aftermath of the Zika and Ebola outbreaks, maternal mortality rose drastically. Addressing gender and complex emergencies, gender and Ebola, and gender and Zika, the authors outline trends within the international response to the crisis and to healthcare systems. The report concludes by arguing that women’s experiences in both the Ebola and Zika outbreaks were extremely different to the experiences of men. The disruption of primary health care services has a disproportionate effect on women and children, in addition to access to resources. The authors argue that in the future, sexual and reproductive health rights in particular must be addressed and is the duty of governments to assist in this. Lastly, gender inequality and discrimination must be brought to the forefront of public health emergency response discussions.