This study examined the mental health of national humanitarian aid workers in northern Uganda and contextual and organizational factors predicting well-being. A cross-sectional survey was conducted among 376 national staff working for 21 humanitarian aid agencies. Over 50% of workers experienced 5 or more categories of traumatic events. Although, in the absence of clinical interviews, no clinical diagnoses were able to be confirmed, 68%, 53%, and 26% of respondents reported symptom levels associated with high risk for depression, anxiety disorders, and posttraumatic stress disorder (PTSD), respectively. Between one quarter and one half of respondents reported symptom levels associated with high risk regarding measured dimensions of burnout. Female workers reported significantly more symptoms of anxiety, depression, PTSD, and emotional exhaustion than males. Workers with the United Nations and related agencies reported fewest symptoms. Higher levels of social support, stronger team cohesion, and reduced exposure to chronic stressors were associated with improved mental health. National humanitarian staff members in Gulu have high exposure to chronic and traumatic stress and high risk of a range of poor mental health outcomes. Given that work-related factors appear to influence the relationship between the two strategies are suggested to support the well-being of national staff working in such contexts.