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Globally gender remains a key factor in differing health outcomes for men and women. This article analyses the particular relevance of gender for debates about global health and the role for international human rights law in supporting improved health outcomes during public health emergencies. Looking specifically at the recent Ebola and Zika outbreaks, what we find particularly troubling in both cases is the paucity of engagement with human rights language and the diverse backgrounds of women in these locations of crisis, when women-specific advice was being issued. We find the lessons that should have been learnt from the Ebola experience have not been applied in the Zika outbreak and there remains a disconnect between the international public health advice being issued and the experience of pervasive structural gender inequalities among those experiencing the crises. In both cases we find that responses at the outbreak of the crisis presume that women have economic, social or regulatory options to exercise the autonomy contained in international advice. The problem in the case of both Ebola and Zika has been that leaving structural gender inequalities out of the crisis response has further compounded those inequalities. The article argues for a contextual human rights analysis that takes into account gender as a social and economic determinant of health.