Fibromyalgia syndrome is a chronic pain condition involving altered nociceptive processing, which requires multidisciplinary management. Photobiomodulation therapy (PBMT) has recently emerged as a promising non-pharmacological approach, but its clinical effectiveness and optimal application methods remain unclear. This systematic review evaluated the efficacy of PBMT in managing Fibromyalgia symptoms, including pain, physical function, sleep quality, and overall well-being, while comparing localized and whole-body delivery. A systematic review was conducted in accordance with the PRISMA guidelines and previously registered on PROSPERO (CRD42024626368). Literature searches were performed across MEDLINE ((PubMed)), PEDro, SPORTDiscus, Scopus, Elsevier (ScienceDirect), and Web of Science (WOS), identifying 17 eligible studies (n = 857 participants). PBMT was applied via low-level laser, infrared, or LED-based devices, delivered either locally or to the whole body. The methodological quality of the studies was assessed using the PEDro scale, and the risk of bias was evaluated using the RoB 2.0 tool. PBMT showed significant clinical benefits, including reduced pain intensity, improved physical function, decreased fatigue, and enhanced quality of life. Whole-body PBMT showed greater and more sustained effects than localized applications, likely due to its systemic modulation of nociceptive pathways and autonomic regulation. Improvements were also observed in terms of psychological well-being, sleep quality, and reduced kinesiophobia. In conclusion, PBMT appears to be an effective therapeutic option for Fibromyalgia syndrome, with whole-body applications offering superior benefits. However, the variability in treatment parameters and study methodologies underscores the need for standardized protocols and high-quality clinical trials to support its integration into multidisciplinary pain management strategies.