Background <p>Headache disorders, including migraine, tension-type headache, and cluster headache, are among the most prevalent and disabling neurological conditions. Although genetic factors contribute to their pathogenesis, they fail to fully account for their clinical heterogeneity, episodic nature, and varied treatment responses. This review synthesizes current evidence on the role of epigenetic mechanisms—including DNA methylation, histone modifications, non-coding RNAs, and RNA modifications—in the pathophysiology of headache disorders.</p> Principal findings <p>Evidence from both human studies and animal models demonstrates that epigenetic mechanisms serve as a dynamic interface between genetic predisposition and environmental triggers. Key findings indicate that stress, sleep disturbances, and hormonal fluctuations can induce specific alterations in DNA methylation and histone acetylation within genes critical to the trigeminovascular system and hypothalamic function, thereby modulating central sensitization and attack susceptibility. Furthermore, distinct profiles of non-coding RNAs have been identified in patient biofluids, correlating with disease state and treatment outcomes, highlighting their potential as clinical biomarkers. The review also synthesizes emerging evidence on how these mechanisms collectively influence cortical spreading depression, neurotransmitter release, and neuroimmune signaling, providing a mechanistic framework for disorder progression and chronification. Importantly, we explore the therapeutic promise of epigenetic drugs and epigenome-editing technologies that are moving from preclinical validation toward early-phase clinical trials for headache management.</p> Conclusion <p>This review advances the understanding of headache disorders by highlighting a dynamic, modifiable layer of regulation at the gene-environment interface. As a promising translational frontier, epigenetics opens new paths for precision medicine and the creation of targeted therapies.</p>