Peacekeepers in United Nations missions experience potentially traumatic events, resulting in increased risk for posttraumatic stress disorder (PTSD). Understanding the course and risk factors of PTSD symptom severity is crucial to ensure personnel safety. To investigate the incidence of PTSD, symptom severity trajectories, and potential risk factors associated with adverse trajectories among Japanese peacekeepers deployed in South Sudan. Data for this 6-year prospective cohort study were collected from December 2011 to December 2018 from Japan Ground Self-Defense Force personnel deployed at the United Nations Mission in South Sudan, corresponding to before and up to 78 months after deployment. Of 3799 potential participants, 80 were excluded because of multiple deployments and 757 because of missing data, incomplete responses, or not providing informed consent. Therefore, 2962 participants were included in the analysis. Data analysis was performed from February 2022 to February 2024. The participants were deployed to United Nations Mission in South Sudan for 6 months. The 22-item Impact of Event Scale-Revised was used to assess PTSD symptoms, with 25 or more points indicating probable PTSD (p-PTSD). Sociodemographic data were collected, and the 30-item General Health Questionnaire was administered before deployment to identify risk factors for PTSD symptom severity. In the 2962 participants studied (2901 [97.9%] male; mean [SD] age, 33.9 [7.2] years), the incidence of p-PTSD was 3.95%. Latent growth mixture models identified 4 symptom severity trajectories: resilient (2143 [72.3%]), recovery (479 [16.2%]), protracted (182 [6.1%]), and delayed (158 [5.3%]). Multinomial logistic regression showed that sleep disturbance was a common risk factor for the 2 most severe trajectories (protracted: odds ratio [OR], 1.29; 95% CI, 1.08-1.54; delayed: OR, 1.26; 95% CI, 1.03-1.53), whereas older age (OR, 1.25; 95% CI, 1.06-1.48), anxiety and dysphoria (OR, 1.45; 95% CI, 1.20-1.75), and general illness (OR, 1.30; 95% CI, 1.06-1.59) were associated with the protracted trajectory. This cohort study found that approximately 4% of the participants developed p-PTSD and identified 4 distinct PTSD symptom trajectories. The findings suggest that addressing sleep disturbance and general health issues could effectively prevent PTSD symptoms among peacekeepers.