Notwithstanding the dramatic admission of the historical injustice against females in the Ethiopian constitution three decades back and the education policy that reflected the enthusiasm to address gender inequality, in practice, it failed to create a fairly inclusive higher education environment that is friendly to women. The aim of this study is to understand the gaps in the existing policy instruments in terms of ensuring gender equality in Ethiopian higher education. The relevant policies and strategies implemented in higher education were examined using women's empowerment frameworks as its analytical lens. The findings reveal that the micro-level policies that are enacted since the mid-1990s until the beginning of 2020s are gradually drifting away from the constitutional promise to make up for past historical injustices against women. This is further complicated by the absence of coherence between system and institutional level policies manifested in the form visible gaps and silences vi-a-vis declared aims to redress gender inequality and inequity in higher education. Finally, the study proposes relevant policy directions to come up with viable gendered instruments at the system and institutional levels.