Examination of prognostic factors for staying at work for long-term sick-listed workers with subjective health complaints (SHC) who partially work in a paid job, and to evaluate whether these factors are comparable with those of workers with other disorders. We used data of 86 partially sick-listed workers with SHC (57 females, 29 males, mean age 47.1 years) and 433 with other disorders (227 females, 206 males, mean age 50.9 years), from an existing prospective cohort study consisting of 2593 workers aged 18–65 years and registered as sick-listed with different health complaints or disorders for at least 84 weeks in the database of the Dutch Social Security Institute. We performed univariable logistic regression analyses (p ≤ 0.157) for all independent variables with the dependent variable staying at work for the workers with SHC. We then performed multivariable logistic regression analyses with forward selection (p ≤ 0.157) and combined the remaining factors in a final, multivariable model (p ≤ 0.05), which we also used for logistic regression analysis in the workers with other disorders. The following factors were significant prognostic factors for staying at work for workers with SHC: full work disability benefits (odds ratio (OR) 0.07, 95% confidence interval (95% CI) 0.01–0.64), good mental health (OR 1.08, 95% CI 1.02–1.14), positive expectations for staying at work (OR 6.49, 95% CI 2.00–21.09), previous absenteeism for the same health complaint (OR 0.31, 95% CI 0.10–0.96) and good coping strategies (OR 1.13, 95% CI 1.04–1.23). For workers with other disorders, full work disability benefits, good mental health and positive expectations for staying at work were also prognostic factors for staying at work. Individual and policy factors seem to be important for staying at work of sick-listed workers with SHC and those with other disorders alike, but several biopsychosocial factors are particularly important for workers with SHC.