Studies on conflict-related sexual violence (CRSV) emphasize the need for the integration of a victim-centered lens into Feminist International Relations (IR) frameworks on sexual violence victimization in conflict or war. However, our understanding of the perpetrator-centered lens is limited. Drawing from ethnographic accounts of Nigerian security agents, male victims of CRSV, and aid workers, we analyze moral injury as a framework for discussing CRSV. In Nigeria, counterterrorism operations can lead to morally detrimental circumstances due to the government’s poor management of counterterrorism operations, resulting in the loss of lives and subsequent feelings of betrayal, anger, and guilt by security agents. Some security agents often display these emotions through violent acts to others, such as CRSV against men and boys suspected of terrorism, thereby exacerbating moral injury. The guilt-based moral injury arises when security agents witness CRSV against men and boys by colleagues and fail to seek justice for victims, as this contradicts social and institutional norms. Our article broadens the concept of moral injury by elucidating its significance to CRSV. In doing so, it advances the concept’s disciplinary focus on psychology to IR or international security—counterterrorism and CRSV—for conceptual sophistication and interdisciplinary exchange of thoughts. This article offers valuable insights into trauma-informed international humanitarian interventions for security agents and victims.