Background <p>Spinal cord injury (SCI) often leads to persistent pain and significant challenges in personal, social, and occupational life, requiring interdisciplinary rehabilitation. Despite advances in pain understanding, effective treatment for the impact of pain on daily living remains sparse. This study addresses the need for effective interventions with the aim of developing and testing an interdisciplinary values-based cognitive behavioral therapy (V-CBT) program for individuals with SCI and persistent pain, also with an objective to apply fine-grained data collection to explore effects and change processes.</p> Methods <p>This study is a replicated multiple baselines single-case experimental design (SCED). Nine participants with SCI and persistent pain will be block-randomized to 1, 2, or 3-week baseline phases, thus serving as their own controls. The intervention comprises a manualized V-CBT program with 10 sessions, delivered online or face-to-face based on participant preference, by an interdisciplinary team (psychologist and physiotherapist). The main aim of the intervention is to promote value-based behaviors. Data collection includes daily online self-reports as well as measurements at pre-treatment, post-treatment, and three-month follow-up. Structured visual analysis and statistical methods assess treatment effects, emphasizing within-case changes and individual responses.</p> Discussion <p>This study possesses several strengths and limitations. A key strength is the interdisciplinary team, consisting of experienced physiotherapists and a psychologist, ensuring a high standard of care. The SCED methodology enables detailed tracking of individual treatment responses, allowing for a nuanced analysis of efficacy and change processes. The integration of a pre-post design with a three-month follow-up enhances the study’s robustness, while the relatively large sample size for a SCED study strengthens its reliability. Additionally, the optional online format improves accessibility for individuals with mobility challenges or those in remote areas, potentially increasing participation and adherence. However, limitations include the absence of professionals such as occupational therapists or physicians, which could provide a more holistic rehabilitation approach. The online format, while increasing reach, may introduce technical barriers and limit therapeutic engagement. SCED designs also require frequent data collection, which may lead to participant fatigue and dropout, impacting data completeness. Despite these challenges, the study offers valuable insights into SCI pain management.</p> Trial registration <p>NCT06599632 (Clinicaltrials.gov; registered 13 September 2024).</p>