Universities and other institutions of higher education in Nigeria see themselves as liberal and open-minded. They support social movements that encourage principles of democracy and social justice, yet their mode of governance is male dominated and patriarchal. This study, therefore, identified the causes of gender inequality in academia and the implications on the academic development of females in the university system. This study was considered necessary because of the observed anomaly in the composition of academic staff in Nigerian universities. Data for the study were obtained from both primary and secondary sources. Primary data were obtained through the in-depth interview of sixty (60) purposively selected male and female academic staff occupying key positions in three (3) Federal universities located in southwestern Nigeria. The study revealed that the recruitment and selection practices in the universities neither stressed male ideology nor discriminated against women; rather merit was the yardstick for acceptance into the profession. It was found that lack of mentoring, poor remuneration, women's lack of interest in academia, family responsibilities, the lengthy period of training, and the ideology that women should have low career aspirations due to traditional roles ascribed to them, accounted for the observed disparity in academia. The implication of this disparity on the academic development of women is the general reduction in their research output and the perpetuation of their low status in academia. The study concluded that appropriate institutional adjustments and affirmation action programmes are necessary to meet women's demands of equality and improve retention.