Background: To investigate the effect of neck-specific exercise with (NSEB) or without (NSE) a behavioural approach and prescribed physical activity (PPA) on general pain disability and psychological factors in chronic whiplash-Associated disorders (WAD), grade 2 and 3, with a 2-year follow-up. Methods:A randomized controlled multi-centre study of 3 exercise interventions (NSE, NSEB or PPA) including a 2-year follow-up. A total of 216 volunteers with chronic WAD were recruited and 194 were analyzed, mean age 40.4 (Standard Deviation [SD] 11.4). Measures of general pain disability, pain catastrophizing, anxiety and depression, and kinesiophobia were evaluated at baseline, and 3, 6, 12 and 24 months with linear mixed models. Results: General pain disability decreased by 28% in the NSEB group from baseline to 3 months (P<0.001) and the improvements in disability were maintained over time (6, 12 and 24 months P<0.01) compared to the NSE (P>0.42) and PPA groups (P>0.43). Pain catastrophizing decreased in the NSE group from baseline to 6 and 12 months (P<0.01) and in the NSEB group from baseline to 3 and 24 months (P<0.01) compared to the PPA group (P>0.82) that showed no change over time. The NSE group improved in kinesiophobia over time from baseline to12 months (P<0.01) compared to the NSEB (P=0.052) and the PPA groups (P>0.74). Anxiety decreased over time from baseline to 12 and 24 months in the NSE group (P>0.02), but not in the NSEB (P>0.25) or the PPA (P>0.50) groups. The PPA had no effect on general disability or any of the measured psychological factors. Conclusion: This randomised controlled trial with a 2-year follow-up shows that physiotherapist-led neck-specific exercise with or without the addition of a behavioural approach had superior outcome on general disability and most psychological factors compared to the mere prescription of physical activity.