Equitable educational access and opportunities are indispensable in creating just societies, particularly developing ones such as Pakistan. This study examines the socio-historical causes and effects of a deeply segregated, class-based primary and secondary education system which has led to Madrassas, religious seminaries, becoming an education system primarily for the poor, thus creating challenges for its graduates in pursuing higher education and in accessing opportunities of social mobility after graduating from Madrassas. Through online surveys of forty-five participants and eight interviews, this ethnographic study brings out the perspectives of Madrassa graduates regarding educational inequities particularly in higher education, the causes of marginalisation of Madrassas and value of Madrassas as an Indigenous knowledge system. The value of Madrassas and the inequities their students experience, are interpreted using the causal theoretical frameworks of post-colonialism, Indigenous knowledge system and structural inequality. The reflective, descriptive, and change-based stories may inform decision makers and contribute to the development of policies which address the intractable social problems experienced by these students falling through the cracks and thus be a step towards exploring a relevant, inclusive, and quality higher education option for this forgotten youth.