Background. Whiplash is the most common injury following a motor vehicle accident. Approximately 60% of people suffer persistent pain and disability six months post injury. Two forms of exercise; specific motor relearning exercises and graded activity, have been found to be effective treatments for this condition. Although the effect sizes for these exercise programs, individually, are modest, pilot data suggest much larger effects on pain and disability are achieved when these two treatments are combined. The aim of this study is to investigate the effectiveness and cost-effectiveness of this comprehensive exercise approach for chronic whiplash. Methods/Design. A multicentre randomised controlled trial will be conducted. One hundred and seventy-six participants with chronic grade I to II whiplash will be recruited in Sydney and Brisbane, Australia. All participants will receive an educational booklet on whiplash and in addition, those randomised to the comprehensive exercise group (specific motor relearning and graded activity exercises) will receive 20 progressive and individually-tailored, 1 hour exercise sessions over a 12 week period (specific motor relearning exercises: 8 sessions over 4 weeks; graded activity: 12 sessions over 8 weeks). The primary outcome to be assessed is pain intensity. Other outcomes of interest include disability, health-related quality of life and health service utilisation. Outcomes will be measured at baseline, 14 weeks, 6 months and 12 months by an assessor who is blinded to the group allocation of the subjects. Recruitment is due to commence in late 2009. Discussion. The successful completion of this trial will provide evidence on the effectiveness and cost-effectiveness of a simple treatment for the management of chronic whiplash. Trial registration. ACTRN12609000825257.