Indomethacin, as a member of the non-steroidal anti-inflammatory drug class, plays a special role in the treatment of headaches. By definition, it is completely efficacious in the treatment of the primary headache disorders paroxysmal hemicrania and hemicrania continua. Therefore, indomethacin is also used as a tool for differential diagnosis in headache clinics. Indomethacin has a clear action as a cyclooxygenase inhibitor. Additional mechanisms and interactions with cell signaling pathways and inflammatory pathways are considered in this article. However, it is not known what mechanism or interaction with pathophysiological mechanisms is the key to indomethacin's specific pharmacology in headache therapy. Focusing on headache therapy, we summarize the current knowledge of pharmacology, treatment options, and recommendations for the use of indomethacin in primary headaches. New findings from the field of headache research, as well as from Alzheimer's disease and cancer research on the pharmacological actions of indomethacin and their potential implications on the pathophysiology of indomethacin sensitive headaches, are discussed.