Purpose The aim of this study was to develop prediction models to determine the risk of sick leave due to musculoskeletal disorders (MSD) in non-sick listed employees and to compare models for short-term (i.e., 3 months) and long-term (i.e., 12 months) predictions. Methods Cohort study including 49,158 Dutch employees who participated in occupational health checks between 2009 and 2015 and sick leave data recorded during 12 months follow-up. Prediction models for MSD sick leave within 3 and 12 months after the health check were developed with logistic regression analysis using routinely assessed health check variables. The performance of the prediction models was evaluated with explained variance (Nagelkerke’s R-square), calibration (Hosmer–Lemeshow test) and discrimination (area under the receiver operating characteristic curve, AUC) measures. Results A total of 376 (0.8%) and 1193 (2.4%) employees had MSD sick leave within 3 and 12 months after the health check. The prediction models included similar predictor variables (educational level, musculoskeletal complaints, distress, supervisor social support, work-home interference, intrinsic motivation, development opportunities, and work pace). The explained variances were 7.6% and 8.8% for the model with 3 and 12 months follow-up, respectively. Both prediction models showed adequate calibration and discriminated between employees with and without MSD sick leave 3 months (AUC = 0.761; Interquartile range [IQR] 0.759–0.763) and 12 months (AUC = 0.740; IQR 0.738–0.741) after the health check. Conclusion The prediction models could be used to determine the risk of MSD sick leave in non-sick listed employees and invite them to preventive consultations with occupational health providers.