This study examines the relationship between institutional autonomy and the security of higher education institutions from violent and coercive attacks. The paper includes a review of the limited literature available, as well as a series of examples illustrating different forms of attacks. These include arrests related to classroom content in Zimbabwe, sectarian divisions in Iraq, impunity for murders of academics in Pakistan, and physical intimidation on campuses in Tunisia. The study suggests that institutional autonomy plays a direct and indirect protective function. It directly helps protect systems of higher education from government interference, making it more difficult for states to act as perpetrators. It also indirectly helps preserve higher education against actual and perceived politicization and ideological manipulation, which in turn might help insulate it from attacks by nonstate parties. The study suggests a framework for examining questions of autonomy and security which in turn suggests a need to develop strategies aimed at increasing autonomy and security simultaneously. This necessarily requires approaches aimed at encouraging states to fulfill their obligations not to engage in or to be complicit in attacks (negative obligations) and obligations to protect higher education from attack and to deter future attacks by holding perpetrators accountable (positive obligations). The study concludes with brief recommendations on how different stakeholders might work to encourage greater understanding and implementation of these obligations, including further research, expert roundtables and information-sharing, development of guidelines and related advocacy campaigns.