BackgroundChronic low back pain is the most frequent pain condition in Veterans and causes substantial suffering, decreased functional capacity, and lower quality of life. Symptoms of post-traumatic stress, depression, and mild traumatic brain injury are highly prevalent in Veterans with back pain. Yoga for low back pain has been demonstrated to be effective for civilians in randomized controlled trials. However, it is unknown if results from previously published trials generalize to military populations.Methods/designThis study is a parallel randomized controlled trial comparing yoga to education for 120 Veterans with chronic low back pain. Participants are Veterans ≥18 years old with low back pain present on at least half the days in the past six months and a self-reported average pain intensity in the previous week of ≥4 on a 0–10 scale. The 24-week study has an initial 12-week intervention period, where participants are randomized equally into (1) a standardized weekly group yoga class with home practice or (2) education delivered with a self-care book. Primary outcome measures are change at 12 weeks in low back pain intensity measured by the Defense and Veterans Pain Rating Scale (0–10) and back-related function using the 23-point Roland Morris Disability Questionnaire. In the subsequent 12-week follow-up period, yoga participants are encouraged to continue home yoga practice and education participants continue following recommendations from the book. Qualitative interviews with Veterans in the yoga group and their partners explore the impact of chronic low back pain and yoga on family relationships. We also assess cost-effectiveness from three perspectives: the Veteran, the Veterans Health Administration, and society using electronic medical records, self-reported cost data, and study records.DiscussionThis study will help determine if yoga can become an effective treatment for Veterans with chronic low back pain and psychological comorbidities.Trial RegistrationClinicalTrials.gov: NCT02224183Electronic supplementary materialThe online version of this article (doi:10.1186/s13063-016-1321-5) contains supplementary material, which is available to authorized users.