Half of individuals with a whiplash injury experience ongoing pain and disability. Many are insufficiently active for good health, increasing their risk of preventable morbidity and mortality, and compounding the effects of the whiplash injury. This paper describes a protocol for evaluating the efficacy of a physical activity promotion intervention in adults with whiplash associated disorders. A multiple-baseline, single case experimental design will be used to evaluate the effects of a physical activity (PA) intervention that includes evidence-based behaviour change activities and relapse prevention strategies for six adults with chronic whiplash. A structured visual analysis supplemented with statistical analysis will be used to analyse: accelerometer-measured PA, confidence completing PA in the presence of neck pain, and pain interference.