Ensuring gender equality in higher education system is high on the agenda worldwide particularly in science disciplines. This study explores the problems and prospects of gender equality in public higher education institutions of Ethiopia, especially in science, technology, engineering, and mathematics. Descriptive survey and analytical research methods were used in the study. Subjects of the study consisted of university instructors, higher education institutions gender affairs officers, and female students. Gender-related policy documents were also used as sources of data. Questionnaire, interviews, and documents analyses were employed as tools of data collection. The data were analysed using mixed methods. The study revealed a serious under representation of female students in science disciplines in the contemporary Ethiopian public higher learning institutions. The paper discusses both the core factors that discourage women from pursuing sciences and suggestions which may assist them join and succeed in sciences.