Gender budgeting is relatively unexplored in the context of higher education and research. In this chapter gender budgeting is employed both as a theoretical and a methodological tool, in order to explore how new managerial approaches and instruments impact the gendered dimensions of precariousness in academic and scientific institutions. Drawing on multiple data collection methods, the implicit and explicit gendered impact of the budget on early career researchers is made visible. We will argue that the financial and managerial procedures and processes employed in higher education favour STEM subjects rather than SSH subjects in relation to research and teaching. This bias impacts earl-career researchers in STEM and SSH disproportionately, with STEM being able to provide more advantageous positions and conditions for early career researchers than SSH. By rewarding male dominated fields and male dominated positions over the more feminised fields and positions, it sustains the historically gendered power relations in higher education and science. By highlighting these gendered implications and consequences we want to direct the attention to need for identifying possibilities for redistribution and actively correcting imbalances and utilising gender budgeting as an instrument for advancing gender equality in academia and science.