© 2015 Miller et al. Background: Previous research suggests that self-management programs for people with chronic pain improve knowledge and self-efficacy but result in negligible effects on function. This study will investigate the effectiveness self-management support with pain science education and exercise on improving function for people with chronic pain in comparison to a wait-list control. A secondary objective is to determine which variables help to predict response to the intervention. Methods/Design: This study will be an unblinded, randomized controlled trial with 110 participants comparing a 6-week program that includes self-management support, pain science education and exercise to a wait-list control. The primary outcome will be function measured by the Short Musculoskeletal Function Assessment - Dysfunction Index. Secondary outcomes will include pain intensity measured by a numeric pain rating scale, pain interference measured by the eight-item PROMIS pain interference item-bank, how much patients are bothered by functional problems measured by the Short Musculoskeletal Function Assessment - Bother Index, catastrophic thinking measured by the Pain Catastrophizing Scale, fear of movement/re-injury measured by the 11-item Tampa Scale of Kinesiophobia, sense of perceived injustice measured by the Injustice Experience Questionnaire, self-efficacy measured by the Pain Self-Efficacy Questionnaire, pain sensitivity measured by pressure pain threshold and cold sensitivity testing, fatigue measured by a numeric fatigue rating scale, pain neurophysiology knowledge measured by the Neurophysiology of Pain Questionnaire, healthcare utilization measured by number of visits to a healthcare provider, and work status. Assessments will be completed at baseline, 7 and 18 weeks. After the 18-week assessment, the groups will crossover; however, we anticipate carry-over effects with the treatment. Therefore, data from after the crossover will be used to estimate within-group changes and to determine predictors of response that are not for direct between-group comparisons. Mixed effects modelling will be used to determine between-group differences for all primary and secondary outcomes. A series of multiple regression models will be used to determine predictors of treatment response. Discussion: This study has the potential to inform future self-management programming through evaluation of a self-management program that aims to improve function as the primary outcome. Trial registration: ClinicalTrials.gov NCT02422459 , registered on 13 April 2015.