Background: Non-specific chronic low back pain (NSCLBP) has become a significant problem due to high healthcare utilization, rising costs or care and perceived limitations of effectiveness of many current treatments. Systematic reviews have repeatedly concluded that, on average across participants, exercise for NSCLBP appears effective in decreasing pain and improving function. Not all people with NSCLBP benefit from exercise programs and it would assist care-providers and care-seekers if factors that impact on program effectiveness and success were identified. Methods and design: The study will be randomised controlled trial comparing an exercise rehabilitation program informed by a participant preferences questionnaire compared to a program without this guideline for patients with chronic low back pain. A sample of 150 patients will be recruited in Melbourne, Australia through community-based healthcare clinics that provide supervised exercise rehabilitation programs for people with non-specific chronic low back pain. Clinicians will be randomly assigned to exercise preferences questionnaire or no questionnaire and participants will be allocated in a concealed manner. A qualitative focus group study of exercise instructor feedback about the exercise preferences instrument will be embedded in the research design. Two qualitative focus group studies will also be conducted for participants in the intervention and the control groups to obtain feedback about participants experiences of the two types of exercise programs. The primary outcomes will be functional ability, pain, fear avoidance, exercise adherence. Discussion: This trial will evaluate the effectiveness of individualised exercise prescription compared to usual exercise prescription for NSCLP and, using feedback following the trial, refine the exercise preferences questionnaire.