The Nigerian university system stands at a critical juncture. Since its establishment during the colonial era, the university has been modelled on Western paradigms that systematically marginalise indigenous knowledge systems (IKS). This epistemic injustice, this paper argues, is not a contingent feature of Nigerian higher education but is constitutive of its postcolonial structure. Drawing on Miranda Fricker's concept of epistemic injustice (testimonial and hermeneutical) and the decolonial literature on epistemicide (Boaventura de Sousa Santos), the paper examines how Nigerian universities perpetuate a form of epistemic violence against indigenous ways of knowing. Using case studies of Ifá divination (Yoruba knowledge system), Bekwarra agrarian philosophy, and traditional ecological knowledge in the Niger Delta, the paper demonstrates that IKS are not pre‑logical or proto‑scientific but constitute sophisticated epistemological systems with their own criteria for justification, standards of evidence, and practices of inquiry. The paper analyses the colonial history of Nigerian university education, the persistence of Eurocentric curricula, and the structural barriers to the legitimation of IKS. It argues that the exclusion of IKS from Nigerian higher education is not merely a matter of cultural loss but constitutes a form of epistemic violence that harms both the knowers whose knowledge is devalued and the broader society deprived of alternative epistemic resources. The paper concludes with a proposal for the decolonial transformation of the Nigerian university through the integration of IKS into curricula, research methodologies, and assessment practices, grounded in the principles of epistemic justice and cognitive decolonisation. It argues that such transformation is not only an ethical imperative but an intellectual necessity for addressing Nigeria's most pressing challenges, from environmental degradation to healthcare delivery to sustainable agriculture.