Background. Musculoskeletal disorders are common and costly disorders to workers compensation and motor accident insurance systems and are a leading contributor to the burden of ill-health. In Australia, vocational rehabilitation is provided to workers to assist them to stay in, or return to work. Self-management training may be an innovative addition to improve health and employment outcomes from vocational rehabilitation. Methods/Design. The research plan contains mixed methodology consisting of a single blind randomised controlled trial, an economic evaluation and qualitative research. Participants (n = 366) are volunteers with compensated musculoskeletal disorders of 3 months to 3 years in duration who were working at the time of the injury/onset of the chronic disorder. The trial tests the effectiveness of usual vocational rehabilitation plus the Chronic Disease Self-Management Program (CDSMP) to which two additional and newly-developed modules have been added, against vocational rehabilitation alone (control) The modules added to the CDSMP focus on how to navigate through compensation systems and manage the return to work process, and aim to be relevant to those in a vocational rehabilitation setting. The primary outcome of this study is readiness for return to work which will be evaluated using the Readiness for Return-to-Work scale. Secondary outcomes include return to work status, health efficacy (heiQ questionnaire) and general health status (SF-12v2 Health Survey). Measures will be taken at baseline, immediately post-intervention and at 6-and 12-months post-intervention by an independent assessor. An economic evaluation will compare the costs and outcomes between the intervention and control groups in terms of cost-effectiveness and a partial cost-benefit or cost analysis. The impact of the intervention will also be evaluated qualitatively, in terms of its acceptability to stakeholders. Discussion. This article describes the protocol for a single blind randomised controlled trial with a one year follow-up. The results will provide evidence for the addition or not of self-management training within vocational rehabilitation for chronic compensated musculoskeletal disorders. Trial Registration. Australia and New Zealand Clinical Trials Registry ACTRN12609000843257.