Pain affects quality of life and can result in absence from work. Treatment and/or prevention strategies for musculoskeletal pain-related long-term sick leave are currently undertaken in several health sectors. Moreover, there are few evidence-based guidelines for such treatment and prevention. The aim of this study is to evaluate the efficacy of 'Tailored Physical Activity' or 'Chronic Pain Self-Management Program' for sick-listed citizens with pain in the back and/or the upper body. This protocol describes the design of a parallel randomised controlled trial on the efficacy of 'Tailored Physical Activity' or a 'Chronic Pain Self-management Program' versus a reference group for sick-listed citizens with complaints of pain in the back or upper body. Participants will have been absent from work due to sick-listing for 3 to 9 weeks at the time of recruitment. All interventions will be performed at the 'Health Care Center' in the Sonderborg Municipality, and a minimum of 138 participants will be randomised into one of the three groups.All participants will receive 'Health Guidance', a (1.5-hour) individualised dialogue focusing on improving ways of living, based on assessments of risk behavior, motivation for change, level of self-care and personal resources. In addition, the experimental groups will receive either 'Tailored Physical Activity' (three 50-minute sessions/week over 10 weeks) or 'Chronic Pain Self-Management Program' (2.5-hours per week over 6 weeks). The reference group will receive only 'Health Guidance'.The primary outcome is the participants' sick-listed status at 3 and 12 months after baseline. The co-primary outcome is the time it takes to return to work. In addition, secondary outcomes include anthropometric measurements, functional capacity and self-reported number of sick days, musculoskeletal symptoms, general health, work ability, physical capacity, kinesiophobia, physical functional status, interpersonal problems and mental disorders. There are few evidence-based interventions for rehabilitation programmes assisting people with musculoskeletal pain-related work absence. This study will compare outcomes of interventions on return to work in order to increase the knowledge of evidence-based rehabilitation of sick-listed citizens to prevent long-term sick-leave and facilitate return to work. The trial is registered in the ClinicalTrials.gov, number NCT01356784.