Background: Most previous attempts to determine the psychological cost of military deployment have been limited by reliance on convenience samples, lack of pre-deployment data or confidentiality and cross-sectional designs. Aims: This study addressed these limitations using a population-based, prospective cohort of US military personnel deployed in support of the operations in Iraq and Afghanistan. Method: The sample consisted of US military service members in all branches including active duty, reserve and national guard who deployed once (n = 3393) or multiple times (n = 4394). Self-reported symptoms of post-traumatic stress were obtained prior to deployment and at two follow-ups spaced 3 years apart. Data were examined for longitudinal trajectories using latent growth mixture modelling. Results: Each analysis revealed remarkably similar post-traumatic stress trajectories across time. The most common pattern was low-stable post-traumatic stress or resilience (83.1% single deployers, 84.9% multiple deployers), moderate-improving (8.0%, 8.5%), then worsening-chronic post-traumatic stress (6.7%, 4.5%), high-stable (2.2% single deployers only) and high-improving (2.2% multiple deployers only). Covariates associated with each trajectory were identified. Conclusions: The final models exhibited similar types of trajectories for single and multiple deployers; most notably, the stable trajectory of low post-traumatic stress pre- to post-deployment, or resilience, was exceptionally high. Several factors predicting trajectories were identified, which we hope will assist in future research aimed at decreasing the risk of post-traumatic stress disorder among deployers.