Objective Many employees have high physical exertion at work and suffer from musculoskeletal pain (MSP) leading to sickness absence with large costs. Participatory ergonomics is a potentially effective intervention for reducing physical exertion, MSP and sickness absence. The main aim of this study was to investigate the effectiveness of a 20-week workplace participatory ergonomic intervention among childcare workers on physical exertion and MSP. Methods In a two-arm cluster-randomized trial, 190 workers were recruited from 16 childcare institutions and randomly assigned to either a 20-week participatory ergonomics intervention consisting of three training workshops or a control group receiving usual care. Primary outcomes were physical exertion during work, maximal pain intensity, number of pain regions, and pain-related work interference. Secondary outcomes were MSP-related sickness absence, need for recovery (NFR), employee involvement, and self-efficacy. We followed the intention-to-treat principle and adhered to the registered study protocol (ISRCTN10928313). Results After 20 weeks, half the workers noticed some positive changes in their work. However, there were no statistically discernible effects in physical exertion, maximum pain intensity, pain-related work interference, or number of pain regions. We found a significant reduction of MSP-related sickness absence in the intervention compared to the control group [-0.48 days per month (95% confidence interval (CI), -0.8- -0.1]. We found no significant effects in NRF or involvement of employees, but self-efficacy was reduced in the intervention compared to the control group [-0.2 (95% CI, -0.3- -0.0)]. Conclusion This 20-week training for a participatory ergonomic intervention in childcare workers did not show effects on physical exertion and MSP, but was both feasible and effective in reducing MSP-related sickness absence.