Fibromyalgia is a chronic nociplastic pain syndrome affecting 2–4% of the global population, with marked female predominance, substantial functional impairment, and an incompletely understood pathophysiology. Diagnosis still relies on symptom-based criteria, and treatment options remain limited. Over the past decade, evidence has positioned the gut–brain axis as a key pathway linking intestinal microbiome dysbiosis, altered microbial metabolites, peripheral immune activation, and central nervous system dysfunction. This review synthesizes current findings across four domains: (i) neurobiological mechanisms by which gut-derived signals influence central sensitization, neuroinflammation, neurotransmitter balance, and neuroendocrine function; (ii) microbiome compositional changes and their metabolic consequences, particularly involving short-chain fatty acids and secondary bile acids; (iii) bidirectional relationships between gut dysbiosis and the psychological comorbidities associated with fibromyalgia; and (iv) limitations of current diagnostic criteria and the potential of multimodal biomarker panels. Evidence from translational animal models, human observational studies, and early-phase trials indicates that gut microbiota contribute to pain perception and psychological symptoms through metabolite-mediated immune and neuroendocrine pathways, although the human evidence remains predominantly associative. Fecal microbiota transplantation, synbiotic supplementation, and metabolite-targeted strategies have shown promising therapeutic potential but remain constrained by small sample sizes, methodological heterogeneity, and a lack of placebo-controlled trials. Microbiome signatures, bile acid profiles, and proteomic markers show promise as adjunctive diagnostic tools but require validation in large, diverse cohorts. Although the field presents compelling mechanistic evidence, methodological limitations must be addressed before these findings can be translated into clinical practice. Overall, microbiome-directed therapies and multimodal biomarker panels represent promising strategies for precision management of fibromyalgia but require rigorous clinical validation.