Abstract Background The prevalence of musculoskeletal pain is high among healthcare workers. Knowledge about risk factors at work is needed to efficiently target preventive strategies. This study estimates the prognosis for recovery from long-term musculoskeletal pain in different body regions among healthcare workers with different levels of perceived physical exertion during healthcare work. Methods Prospective cohort study among 4,977 Danish female healthcare workers responding to a baseline and follow-up questionnaire in 2005 and 2006, respectively. We defined long-term pain, short-term pain and pain-free as > 30, 1–30 and 0 days with pain during the last year, and included in the analyses only those with long-term pain at baseline in the low back (N=1,089), neck/shoulder (N=1,400) and knees (N = 579), respectively. Using cumulative logistic regression analysis, the prognosis for recovering from long-term pain at baseline to short-term pain or pain-free at follow-up in the respective body regions when experiencing moderate or light (reference: strenuous) physical exertion during healthcare work was modeled. Results Among those with long-term pain at baseline 34% (low back), 29% (neck/shoulders), and 29% (knees) recovered to short-term pain at follow-up and 7% (low back), 8% (neck/shoulders), and 17% (knees) recovered to being pain-free. After adjusting for potential confounders (age, BMI, tenure, smoking status, leisure physical activity and psychosocial work conditions), light perceived physical exertion during healthcare work was associated with improved prognosis for recovery from long-term pain in the low back (OR 1.42, 95% CI 1.01 – 1.99) and neck/shoulders (OR 1.89, 95% CI 1.43 – 2.50), but not in the knees. Moderate physical exertion was not associated with improved prognosis for recovery from long-term pain for any of the body regions. Conclusion In the present study, healthcare workers with light perceived physical exertion during healthcare work had the best prognosis for recovery from long-term pain in the low back and neck/shoulders. This suggests that efforts to reduce perceived exertion during work may improve recovery from chronic pain.