This study aimed to compare the effect on self-rated pain, disability and self-efficacy of three interventions for the management of chronic Whiplash Associated Disorders (WAD): physiotherapist-led neck-specific exercise, physiotherapist-led neck-specific exercise with the addition of a behavioral approach, or prescription of physical activity. Two hundred and sixteen persons with chronic WAD volunteered to participate in this randomized, assessor blinded, clinical trial of three exercise interventions. Self-rated pain/pain bothersomeness (Visual Analogue Scale), disability (Neck Disability Index) and self-efficacy (Self-Efficacy Scale) were evaluated at baseline and at three and six months. The proportion of patients reaching substantial reduction in pain bothersomness (at least 50% reduction) was more evident (P<0.01) in the two neck-specific exercise groups (29-48%) compared to the prescription of physical activity group (5%) at three months. At six months 39-44% of the patients in the two neck-specific groups and 28% in the prescription of physical activity group reported substantial pain reduction. Decrease in disability was also larger in the two neck-specific exercise groups at both three and six months (P<0.02). Self-efficacy was only improved in the neck-specific exercise group without a behavioral approach (P=0.02). Although there were no significant differences in any outcomes between the two physiotherapist-led neck-specific exercise groups. Neck-specific exercise resulted in superior outcomes compared to prescription of physical activity in this study, but the observed benefits of adding a behavioral approach to the implementation of exercise in this study were inconclusive.