Objectives We examined perceptions of institutional betrayal among Veterans exposed to military sexual trauma (MST) and whether perceptions of institutional betrayal are associated with symptoms of posttraumatic stress disorder (PTSD), depression, and suicidal ideation and attempt after MST. Method A total of 49 Veterans with MST completed self‐report measures and interviews in a Veterans Health Administration setting. Results Many participants reported perceptions that a military institution created an environment in which MST seemed common, likely to occur, and did not proactively prevent such experiences. Many participants expressed difficulty reporting MST and indicated that the institutional response to reporting was inadequate. Over two‐thirds perceived that the institution had created an environment in which they no longer felt valued or in which continued membership was difficult. Perceptions of institutional betrayal were associated with PTSD symptoms, depressive symptoms, and increased odds of attempting suicide after MST. In contrast, perceptions of institutional betrayal were not associated with post‐MST suicidal ideation. Among the subsample of Veterans exposed to military sexual assault, the association between institutional betrayal and PTSD symptoms approached significance. Conclusions Perceptions regarding institutional betrayal appear to be highly relevant to MST and its sequelae. These findings underscore the importance of Veterans’ perceptions of the military institution's efforts to prevent and respond to MST to individual recovery from sexual trauma. Additional research regarding the association between institutional betrayal and health‐related outcomes is needed.