The aim of the present study was to compare the effect of increased aerobic capacity versus muscle strength rehabilitation of female hospital staff with long-lasting musculoskeletal back pain. Seventy-nine women agreed to participate in the intervention study. After a medical examination, 65 individuals were assigned to one of three balanced groups: Endurance training (aerobic capacity promoting training: ET: n = 22), strength promotion exercise (SP: n = 24) or a control group (CON: n = 19). The active groups met twice a week for 60 minutes of exercise over 15 weeks. Aerobic capacity (VO2max) and musculoskeletal pain were measured immediately before (T1) and after the intervention period (T2). Aerobic capacity significantly increased in the ET group, whereas no change was observed in the SP group, and a significant reduction was found in the CON group from T1 to T2. Musculoskeletal pain was significantly reduced in both intervention groups, whereas minor changes were observed in the control group. Results from a 7-month follow-up (T3) survey confirmed the beneficial effects of interventions on musculoskeletal pain. In conclusion, improved aerobic capacity appeared not to be a necessary mechanism in musculoskeletal back pain reduction.