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Objective The aim of this study was to clarify the association of fear of movement and physical activity among patients with chronic musculoskeletal pain. Methods The sample comprised 93 patients participating in a multidisciplinary pain management programme. The purpose of the programme was to regain overall functioning by means of physical and functional exercises, education and personal pain management training. Tampa Scale of Kinesio-phobia and Leisure Time Physical Activity questionnaires were completed at baseline, and at 6-month and 12-month follow-ups. Results At baseline, low and medium kinesiophobia groups showed more leisure-time physical activity than did the high kinesiophobia group (p = 0.024). At a 6-month follow-up the high kinesiophobia group had increased their physical activity index to the level of the low and medium kinesiophobia groups and maintained that change to 12-month follow-up. The effect sizes of the change in the physical activity index and pain intensity at the 12-month follow-up were both moderate (0.56) in the high kinesiophobia group. Conclusion The change in physical activity and kinesiophobia was associated with the level of baseline kinesiophobia. Multidisciplinary rehabilitation seems to produce favourable effects in terms of physical activity and pain among the high kinesiophobia patients.