Background The mental health impact of the initial years of military service is an under-researched area. This study is the first to explore mental health trajectories and associated predictors in military members across the first 3–4 years of their career to provide evidence to inform early interventions. Methods This prospective cohort study surveyed Australian Defence personnel (n = 5329) at four time-points across their early military career. Core outcomes were psychological distress (K10+) and posttraumatic stress symptoms [four-item PTSD Checklist (PCL-4)] with intra-individual, organizational and event-related trajectory predictors. Latent class growth analyses (LCGAs) identified subgroups within the sample that followed similar longitudinal trajectories for these outcomes, while conditional LCGAs examined the variables that influenced patterns of mental health. Results Three clear trajectories emerged for psychological distress: resilient (84.0%), worsening (9.6%) and recovery (6.5%). Four trajectories emerged for post-traumatic stress, including resilient (82.5%), recovery (9.6%), worsening (5.8%) and chronic subthreshold (2.3%) trajectories. Across both outcomes, prior trauma exposure alongside modifiable factors, such as maladaptive coping styles, and increased anger and sleep difficulties were associated with the worsening and chronic subthreshold trajectories, whilst members in the resilient trajectories were more likely to be male, report increased social support from family/friends and Australian Defence Force (ADF) sources, and use adaptive coping styles. Conclusions The emergence of symptoms of mental health problems occurs early in the military lifecycle for a significant proportion of individuals. Modifiable factors associated with wellbeing identified in this study are ideal targets for intervention, and should be embedded and consolidated throughout the military career.