Rwanda has made tremendous achievements in improving access of both males and females all levels of education. To this end, reforms and equity measures have been undertaken to promote gender equality within the Rwandan education system. However, while the proportion of female students is quite good at lower levels of education, it shrinks at higher educational ladder. In this perspective, enrollment, participation, completion and achievement rates of girls are still lower at secondary and tertiary levels compared to boys. Another discrepancy is observed in the fields of studies and university of choice. In fact, girls are more likely to enroll in courses related to social studies mostly available in private institutions rather than enrolling in science related courses available in public universities. Furthermore, females are under-represented in both academic and administration positions at secondary and tertiary levels of education. Therefore, the key objectives of this paper were to highlight the progress made towards achievement of gender equality, to identify the factors that contributed to that achievement, and finally to explore what remains a stumbling to full realization of gender parity in Rwandan education system. This paper was mainly a desktop research that used different official documents including statistics yearbooks, reports, and strategic plans among others. The study revealed that the number of girls outnumbered that of boys at lower levels of education, elimination of school fees, reforming curricula and establishing gender sensitive infrastructure contributed to this progress. Poverty and some traditional socio-cultural beliefs are key challenges to gender parity. Government and other stakeholders were recommended to sensitize and encourage girls to enroll in TVT and universities, and provide more gender sensitive infrastructure and amenities.