Consistent economic downturns, political uprisings, and social upheavals from the 1980s have significantly depleted the quality of higher education in Africa, particularly graduate training. While remarkable strides in graduate training have been made in countries such as South Africa relative to other parts of the continent, policy and funding challenges continue to threaten the quality of students and programs. Over the past two decades, new forms of institutional collaborations aimed at revamping graduate training in sub-Saharan Africa have emerged. Debates on how to revamp the higher education system are ongoing among scholars, policymakers, administrators, and funders, but minimal attention is paid to the students’ voices, particularly women’s that speak to the dire conditions under which graduate training is carried out. To spur more discussion about this gap in literature, we conducted focus group discussions with female graduate students in four higher education institutions in Nigeria and South Africa. Our participants identified five major challenges that graduate students often wrestle with: financial challenges, limited sources of and dated curricular materials, institutional infrastructure and program logistics, academic supervision, and gender relations among students as well as between students and scholars. These challenges, our participants assert, often place female graduate students in a more vulnerable position than their male counterparts. Our findings, though preliminary, point to the need to actively engage students, especially women, in academic debates and initiatives aimed at improving graduate training in Africa.