Despite lack of convincing evidence that reduced aerobic fitness is associated with chronic back pain (CBP), exercise programs are regarded as being effective for persons with non-specific CBP. It is unsure whether gain in aerobic fitness following intervention is associated with functioning improvement in persons with CBP. The objective of this prospective cohort study was to study the impact of aerobic fitness on functioning in persons with CBP, at baseline and following 3-week intensive interdisciplinary intervention. This study included persons who had passed 8 weeks of sick-listing because of back pain (n = 94) and were referred to a 3-week intensive biopsychosocial rehabilitation program. Aerobic fitness was assessed with a sub-maximal bicycle test at baseline, at admission to and discharge from the rehabilitation program, and at 6 months follow-up. Contextual factors, body function, activity and participation were evaluated before and after intervention. In addition, working ability was recorded at 3-years followup. At baseline aerobic fitness was reduced in most subjects, but improved significantly following intervention. Baseline measurements and intervention effects did not differ among the diagnostic sub-groups. Neither contextual factors nor functioning at baseline were associated with aerobic fitness. Increase in aerobic fitness was not associated with improvements in functioning and contextual factors and work-return following intervention either. From this study we conclude that improvement of aerobic fitness seems of limited value as goal of treatment outcome for patients with CBP.