Abstract Background Whiplash injury is the most common traffic-related injury affecting thousands of people every year. Conservative treatments have not proven effective in preventing persistent symptoms and disability after whiplash injury. Early established maladaptive pain behaviours within the first weeks after the injury may explain part of the transition from acute to chronic whiplash associated disorder (WAD). Hence, early targeting of psychological risk factors such as pain catastrophizing, fear-avoidance-beliefs, depression, and symptoms of posttraumatic stress disorder (PTSD) may be important in preventing the development of chronic WAD. Some evidence exists that targeting fear-avoidance beliefs and PTSD with exposure strategies and value-based actions may prevent development of persistent disability after whiplash injury. Yet, the results have to be tested in a randomized controlled trial (RCT). The primary objective of the present study is to test whether a specifically tailored value-based cognitive-behavioural therapy program (V-CBT) is able to prevent the development of persistent disability, pain, and psychological distress if delivered within the first three months after a whiplash injury. Methods/design The current study is a two-armed randomized controlled study with a crossover design. Group A is scheduled for V-CBT within one week of randomization and group B with a delayed onset 3 months after randomization. Discussion If the study detects significant effects of V-CBT as a preventive intervention, the study will provide new insights of preventive treatment for patients with WAD and thereby serve as an important step towards preventing the chronic condition. Trial registration Current Controlled Trials Registration September 19, 2014: NCT02251028