Gender inequalities in science persist across the EU member states with the underrepresentation of women in the top echelons of scientific hierarchies. In the past two decades, the European Union tried to address this issue with a mix of policies based on social and economic rationales. The chapter identifies three policy challenges that still persist today: the underrepresentation of women in top positions in science and in decision-making bodies, the gender pay gap, and the absence of gender in research content. The analysis shows that the complexities of actors and the importance of institutional entrepreneurs, networks and advocacy groups have led to a more non-linear policy learning from ‘fixing the women’ to ‘fixing the institutions’ approaches. The chapter points out how the economic rationale has increasingly taken over the social equality rationale regarding gender in research policies. The increased rationalization of research organizations allows the implementation of gender policies, although a lot of implementation stays at the ideational level.