Academic freedom in contexts where the state, universities, and religious institutions shape legitimate knowledge and the boundaries of permissible discourse cannot be assessed merely by counting formal prohibitions; restrictions may range from the rewriting of rules to legal, organizational, and normative pressures. This study examines competition between religious and scholarly authority in Afghanistan and Pakistan and its consequences for academic freedom, asking how structures of political and legal authority translate this competition into different mechanisms and outcomes of restriction. Drawing on historical institutionalism and the organizational field literature, the study employs a structured and focused comparative design. Data comprise governmental and university documents, laws and regulations, reports by international and human rights organizations, and peer-reviewed academic sources from August 2021 to December 2025, coded and compared through systematic and directed document analysis. Findings indicate that in Afghanistan, the concentration of Taliban authority has moved the dominant pattern toward “institutional displacement and replacement,” producing formal, pervasive, and more institutionally entrenched restrictions, particularly on institutional autonomy and freedom of learning. In Pakistan, the evidence is more consistent with a pattern in which the university structure persists and authority remains relatively dispersed, while pressure is channeled primarily through legal, judicial, normative, and self-censorship mechanisms; this pattern approximates “intra-structural restriction” and produces selective and uneven constraints on freedom of research and teaching. Given the potential under-observability of informal restrictions, these findings concern mechanisms that can be substantiated in available documents rather than demonstrating the absence of other forms of restriction.