Research grant funding influences the organisation of academic work and academic careers. We problematise general approaches to gender bias in research grant funding and argue that it fails to include the wider structures of inequality and the unequal gendered power relations in academia. Approaching the subject with gender budgeting we challenge assumed gender-neutral practices. The objective is to illuminate how the gendered funding system and (the previous and subsequent) gendered structures of academia are maintained. The whole grants scheme is assessed, drawing on statistical data collected on the whole population of a medium-size, comprehensive research and educational institution in Iceland, and two types of competitive grants. The data is measured against the pool of applicants and comparisons within and between fields and ranks are made. By including the structures of inequality and the gendered power relations, the results show how the funding system is biased not only in favour of men, but towards the male-dominated and culturally masculine positions and fields. This approach illustrates the need to address the whole academic system in order to challenge the norms that maintain and reproduce gender inequalities.