This article examines the lived experiences of women in Ethiopian higher education (HE) as a counterpoint to understandings of gender equity informed only by data on admission, progression and completions rates. Drawing on a critical qualitative inquiry approach, we analyse and interpret data drawn from focus group discussions with female students and academic women in two public universities in Ethiopia. Individual accounts and shared experiences of women in HE revealed that despite affirmative action policies that slightly benefit females at entry point, gender inequality persists in qualitative forms. Prejudice against women and sexual violence are highlighted as key expressions of qualitative gender inequalities in the two universities. It is argued that HE institutions in Ethiopia are male-dominated, hierarchical and hostile to women. Furthermore, taken-for-granted gender assumptions and beliefs at institutional, social relational and individual levels operate to make women conform to structures of disadvantage and in effect sustain the repressive gender relations.