Chronic migraine, affecting approximately 2% of the global population, markedly diminishes quality of life and imposes significant societal costs, surpassing the impacts of episodic migraine. Conventional medical treatments leave about 30% of patients with persistent chronic migraine, some of whom fluctuate between episodic and chronic migraine states. A holistic, functional medicine approach may provide supplementary benefits for these individuals. Clinical imbalances often identified in chronic migraine patients—such as mitochondrial dysfunction, oxidative stress, gut microbiota dysbiosis, leaky gut syndrome, food intolerance, histamine syndrome, vitamin D deficiency, and autonomic nervous system imbalances—can be detected through specific functional medical assessments, including urine organic acid profiles, hair tissue mineral analysis, hydrogen breath tests, comprehensive blood tests, and heart rate variability tests. Integrative functional medical interventions, encompassing lifestyle modifications, oral and intravenous nutrition therapies, and the comprehensive 5R program (remove, replace, reinoculate, repair, rebalance) for gut health, could offer therapeutic benefits. This review delves into the functional medicine paradigm and its potential role in managing chronic migraine.