Photobiomodulation therapy (PBMT), as an adjunct therapy to exercise, can reduce pain in musculoskeletal disorders. In addition, PBMT associated with exercise decreases fatigue, accelerates muscle recovery and enhances performance and gain through different training protocols. Although it has not been investigated, the association of PBMT and exercise therapy could be an alternative to improve the positive effects of exercise in patients with non-specific low back pain (LBP). Therefore, we aim to evaluate the effects of PBMT associated with motor control exercise (MCE) versus placebo associated with MCE in patients with chronic non-specific LBP. This is a prospectively registered, two-arm, randomised, placebo-controlled, triple-blind trial. A total of 148 patients with chronic non-specific LBP will be randomised to either active PBMT associated with MCE or placebo PBMT associated with MCE. Treatment sessions will be provided twice a week for 6 weeks. The primary outcomes will be pain intensity and general disability measured at the end of the treatment. The secondary outcomes will be pain intensity and general disability measured 1 month after the end of the treatment, 3, 6 and 12 months after randomisation, in addition to levels of prostaglandin E2 measured at the end of the treatment. Medication intake, cointerventions and adverse events will be measured at all time points. This study was approved by the Research Ethics Committee of Irmandade de Santa Casa de Misericórdia de Porto Alegre. The results will be disseminated through scientific publications and presentations at scientific meetings. Trial registration number: NCT05487118.