This article examines the problem of gender inequalities in two science and technology universities in Ethiopia drawing on the lived experiences of academic (teaching and research faculty) women. We analysed the data from in-depth interviews with STEM academic women through reference to Acker's theory of gendered organisation. Our findings demonstrate that women faculty are not only significantly underrepresented but also face gendered barriers that hinder their equitable participation and career progression. Based on these findings, we argue that the gendered institutional structures, practices, processes and cultures of the two universities underpin the perpetuation of both quantitative and qualitative gender inequalities in academe of the two universities. We further argue that it is imperative to acknowledge these institutional impediments and tackle them to redress the persistent gender inequalities in these contexts. The findings of this paper contribute to the existing research by bringing perspectives and experiences of STEM academic women from the Global South context.