Abstract Background Stress-related disorders are common sickness absence (SA) diagnoses in many Western countries. Knowledge of SA and disability pension (DP) patterns among people with such SA is needed. Thus, the aim was to identify future SADP trajectories among people with a new SA spell due to stress-related diagnosis and to examine sociodemographic and health-related factors associated with identified trajectories. Methods Using microdata from nationwide registers, we included all people living in Sweden with a new SA spell >14 days due to stress-related diagnoses (ICD-10 code F43) in 2011 (N = 32,417) or 2018 (N = 65,511), respectively. These two cohorts were followed prospectively for 13 months from the SA spell start, to identify trajectory groups of mean SA/DP days/month using group-based trajectory modeling. We used multinomial logistic regression to explore associations between sociodemographic and health-related predictors and trajectory membership. Results We identified the following SA/DP trajectories in both cohorts: steep drop (30.6% and 35.9% of all included in 2018 and 2011, respectively); fluctuating (8.7%, 11.2%); fast decrease (25.5%, 24.4%); medium decrease (18.1%, 13.1%); slow decrease (10.8%, 7.3%), and constant high (6.2%, 8.0%). Compared to the steep drop trajectory, individuals in the other trajectories were more likely women, older, and had prior SA/DP or secondary outpatient healthcare visits. Starting the SA spell full-time was the strongest predictor for the slow decrease and constant high trajectory, and previous SA or diagnosis of other mental disorders were predictors of the constant fluctuating and constant high trajectory. Conclusions The similarity of the identified trajectories in the two cohorts is a strength. The results reveal the diversity of future SA/DP in this patient group, indicating the importance of identifying patients at risk of long-term SA who might need further interventions early in the process. Key messages • In two population-wide cohorts with a new sickness absence (SA) spell with stress-related diagnoses, six trajectories of SA/disability pension days were identified during the 13-month follow-up. • Most of those in the cohorts had trajectories that ended with no SA/DP after 13 months, while two trajectories, including 15-19% of individuals, showed high or varying SA/DP days during the follow-up.