BACKGROUND: Low back pain affects approximately 80% of people at some stage in their lives. Exercise therapy is the most widely used nonsurgical intervention for low back pain in practice guidelines. Whole body vibration exercise is becoming increasingly popular for relieving musculoskeletal pain and improving health-related quality of life. However, the efficacy of whole body vibration exercise for low back pain is not without dispute. This study aims to estimate the effect of whole body vibration exercise for chronic low back pain. METHODS/DESIGN: We will conduct a prospective, single-blind, randomized controlled trial of 120 patients with chronic low back pain. Patients will be randomly assigned into an intervention group and a control group. The intervention group will participate in whole body vibration exercise twice a week for 3 months. The control group will receive general exercise twice a week for 3 months. Primary outcome measures will be the visual analog scale for pain, the Oswestry Disability Index and adverse events. The secondary outcome measures will include muscle strength and endurance of spine, trunk proprioception, transversus abdominis activation capacity, and quality of life. We will conduct intention-to-treat analysis if any participants withdraw from the trial. DISCUSSION: Important features of this study include the randomization procedures, single-blind, large sample size, and a standardized protocol for whole body vibration in chronic low back pain. This study aims to determine whether whole body vibration exercise produces more beneficial effects than general exercise for chronic low back pain. Therefore, our results will be useful for patients with chronic low back pain as well as for medical staff and health-care decision makers. TRIAL REGISTRATION: Chinese Clinical Trial Registry: ChiCTR-TRC-13003708.