Gender equality in research and innovation is one of the key priorities of the European Research Area and is part of the European Commission Gender Equality Strategy for 2020-2025 (European Commission, 2020). However, research performing organisations (RPOs) in Europe still show persistent gender inequalities with vertical (the glass ceiling phenomenon, with few women being able to reach the top of the ladder) and horizontal segregation (both with reference to the disciplines of research and teaching and in the choice of education fields) (European Commission, 2019a). This paper analyses inequalities in European RPOs and proposes strategies to reduce them. Can gender budgeting (GB) be a tool, along with other specific actions, in achieving gender equality? What key features should GB include to do so? To answer these questions, 25 GB examples from European RPOs were analysed, paying attention to the methodologies and the indicators that were used, and to their interaction with gender equality plans. Viable suggestions are put forward to improve the impact of GB on gender equality outcomes in RPOs.