Abstract Gender is a major factor in Uganda’s higher education system. This manuscript accounts for the conundrum of gender inequality in the system through a comparative multi group analysis of Gender Parity Index in 10 colleges and 158 fields of study. From a sample of 101 ​504 students, admitted in five public universities, from 112 districts, from 2009 to 2017, the study found that even though women in Uganda now participate in higher education in much greater numbers, gender realities on the ground have not changed. In fact, gender inequality in access to higher education has become much more nuanced and complex than was anticipated; half the population of women was found in one of ten colleges; in eight other colleges, men outnumbered women by a ratio of 8:2. Uganda’s higher education system was stereotypic of a system that reinforces the images of women in one field and that of men in another. The study calls for a differentiated approach to policy making, to change the history, customs and traditions of college admission, which remains strongly in favor of men, in order to address the conundrum of gender inequality in Uganda’s higher education system.

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