Water and sanitation facilities in higher education institutions plays a fundamental role in economic activity and human well-being including education. However, there is lack of gender based evidence on the provisioning and management of water and sanitation facilities in higher education institutions in East Africa. This study assessed gender responsiveness in the provisioning and management of water and sanitation facilities at the two East African Universities namely Makerere University in Uganda and University of Dar es Salaam in Tanzania. The study adopted a cross-sectional gender focused study design. Forty (40) in-depth interviews and twenty-four (24) focused group discussions with University managers and student's leaders were conducted. Findings indicated that gender perspectives were inadequately integrated in the provisioning and management of water and sanitation facilities. Inadequacies and gender differences were created with female students and those with special needs receiving limited access to and utilization of water and sanitation facilities than their male student's counterparts.