Background: Whiplash-associated disorder (or "whiplash") is a common condition incurring considerable expense in social and economic terms. A lack of research on effective therapy for patients with chronic whiplash associated disorders prompted the design of the current study. The primary aim of this randomised controlled trial is to determine the effects of a physical activity program for people with chronic (symptoms of > 3 months duration) whiplash. A secondary aim is to determine if pain severity, level of disability and fear of movement/(re)injury predict response to a physical activity program. Methods / Design: This paper presents the rationale and design of a randomised controlled trial examining the effects of advice and individualized sub-maximal exercise programs in the treatment of whiplash associated disorders. Discussion: This paper highlights the design, methods and operational aspects of a significant clinical trial in the area of whiplash and chronic pain.