Background: The development of an integral and global treatment to improve the quality of life in those with fibromyalgia syndrome (FMS) is challenging.Methods: This study is a randomized, placebo-controlled clinical trial. Participants will be recruited in a private care practice and randomized to receive either a whole body Photobiomodulation (PBM) therapy program or placebo. Primary out comes will be pain (NumericPain Rating Scale; Widespread Pain Index; Symptom Severity Score), functionality (Fibromyalgia Impact Questionnaire; The Leisure Time Physical Activity Instrument), quality of soft tissue (elastography) and central sensitisation (pain pressure threshold and the Autonomic Symptom Profile). Secondary outcomes will be psychological factors (Pain Catastrophising scale, Tampa Scale, Self-Efficay questionnaire). Assessments will be at baseline (T1), after session 6 (T2), after treatment (T3) and 2 weeks (T4), 3 (T5) and 6 (T6) month´ follow-up.Discussion: PBM therapy has been shown to reduce pain and inflammation and to increase the rate of tissue repair for a wide range of conditions, but its potential use as a whole body treatment in FM is yet to be explored. This trial will investigate whether whole body PBM therapy is effective at reducing pain intensity, improving functionality, quality of soft tissue, central sensitisation symptoms and psychological measurements. Furthermore, 3 and 6 months follow up will investigate long-term efficacy of this treatment.Trial registration: NCT04248972. Registered on January 29, 2020, https://clinicaltrials.gov/ct2/show/NCT04248972?term=navarro-ledesma+santiago&draw=2&rank=2.