We aimed to investigate the association between work-time compositions of physical behavior and sick leave trajectories due to musculoskeletal pain over one year. We conducted a secondary analysis using the data of 981 workers in a Danish prospective cohort (DPHACTO 2012–2014). At baseline, we assessed physical behaviors (sitting, standing, light physical activity (LIPA), and moderate-to-vigorous physical activity (MVPA)) at work and during leisure, using accelerometers. Over 1 year follow-up, workers reported sick-leave days due to musculoskeletal pain at 4-week intervals. Four distinct trajectories of sick leave were previously identified in this cohort (“no sick leave”, “few days—increasing trajectory”, “some days—decreasing trajectory”, “some days—increasing trajectory”), and used as an outcome in multinomial regression models with work-time compositions as predictors, adjusted for compositions of behavior during leisure, age, sex, body mass index, and smoking habits. More time spent sitting relative to the other behaviors was negatively associated with the trajectory of few days—increasing sick leave (p = 0.004), while time in LIPA was positively associated with the trajectory of some days—increasing sick leave (p = 0.009). Standing and MVPA were not significantly associated with sick leave trajectories. In conclusion, work-time compositions with more sitting relative to the other behaviors had lower risk for an increasing trajectory of sick leave due to pain, while compositions with more LIPA had higher risk. This may have implications for prevention of pain-related sick leave in blue-collar workers.