Background Pain predominant multisymptom illness (pain-CMI) refers to symptom-based conditions where pain is a primary symptom. There is initial evidence that health coaching may be efficacious in treating pain-CMI because it can be tailored to the veteran’s goals and emphasizes long-term behavior change, which may indirectly impact the maintaining factors of pain-CMI (e.g., catastrophizing, poor pain control, and limited activity). This paper describes the study protocol and rationale of a randomized controlled trial that will compare the efficacy of remote-delivered health coaching in reducing disability and pain impairment for veterans with pain-CMI to remote-delivered supportive psychotherapy. Methods This randomized controlled trial will consist of two treatment arms: remote-delivered health coaching and remote-delivered supportive psychotherapy, the active control. Each treatment condition will consist of twelve, weekly one-on-one meetings with a study provider. In addition to the baseline assessment, participants will also complete 6-week (mid-treatment), 12-week (post-treatment), and 24-week (follow-up) assessments that consist of questionnaires that can be completed remotely. The primary aims for this study are to determine whether health coaching reduces disability and pain impairment as compared to supportive psychotherapy. We will also examine whether health coaching reduces physical symptoms, catastrophizing, limiting activity, and increasing pain control as compared to supportive psychotherapy. Discussion This study will contribute to the existing literature on pain-CMI and report the effectiveness of a novel, remote-delivered behavioral intervention.