Sinus headache is not a diagnostic term supported by the academia, yet it appears to be understood by the general public and larger medical community. It can be considered both a primary and secondary headache disorder. As a primary headache disorder, most of the patients considered to have sinus headache indeed have migraine (migraine with sinus symptoms). Yet it is also possible that some attacks of sinus headache may represent a unique clinical phenotype of migraine or be a unique clinical entity. Potentially, primary sinus headache can chronify and be refractory through immune-mediated mechanisms or as a catalyst for migraine chronification through ineffective treatment or medication overuse and misuse. As a secondary headache disorder, sinus headache can be associated with a wide range of underlying etiologies such as infection, anatomical abnormalities, trauma, and immunological disease or sleep disorders. It is possible that these underlying pathophysiological processes generate long-standing activation of nociceptive mechanisms involved in headache and can lead to chronification and refractoriness of the headache symptomatology. This article explores some of the potential mechanisms and the available scientific studies that may explain how sinus headache can become chronic and present to the clinician as a refractory headache disorder.