Abstract Background Previous studies have shown higher long-term sickness absence (LTSA) rates among employees with pain as compared to those not reporting pain. We examined distinct developmental patterns in LTSA (≥10 consecutive working days) among young and early midlife employees with pain at baseline, and factors associated with LTSA trajectories. Methods The study population consisted of 19-39-year-old employees (n = 1685) of the City of Helsinki who reported current pain at baseline in 2017. Data on all-cause LTSA days through March 2020 were collected from the Social Insurance Institution of Finland. Group-based trajectory modelling was used to identify distinct all-cause LTSA trajectories. Multinomial logistic regression was used to examine associations of pain characteristics, lifestyle- and occupational factors with trajectory group membership. Results Three distinct LTSA-trajectory groups were identified; No LTSA (74%), Decreasing (18%), and Increasing (8%). Compared to the No LTSA trajectory, employees in the Decreasing trajectory were more likely to have chronic (OR 1.34, 95% CI 1.04-1.73) or multisite (OR 1.81, 95% CI 1.36-2.41) pain, smoke (OR 1.55, 95% CI 1.18-2.03), have obesity (OR 1.70, 95% CI 1.21-2.38), manual or routine non-manual occupation (OR 1.87, 95% CI 1.31-2.67) and high physical workload (OR 1.47, 95% CI 1.14-1.90), after adjusting for age and gender. Predictors of the Increasing trajectory were not identified. Conclusions Distinct LTSA-trajectories were identified among young and early midlife employees with pain, of whom a majority had no LTSA during follow-up. Chronic and multisite pain, unhealthy lifestyle, lower occupational class, and higher physical workload are related to a pattern with more LTSA. Future intervention studies could examine opportunities to prevent LTSA through supporting younger employees who work with pain and have these risk factors. Key messages • Distinct trajectories of LTSA were identified among younger employees with pain, of whom most had no LTSA. Pain characteristics, lifestyle and occupational factors predicted trajectory membership. • Future intervention studies could examine opportunities to prevent LTSA through support to employees who work with pain and have pain-, lifestyle- and occupation related risk factors of LTSA.