Non-steroidal anti-inflammatory drugs, cyclo-oxygenase inhibitors, are used routinely in the treatment of primary headache disorders. Indomethacin is unique in its use in the diagnosis and treatment of hemicrania continua and paroxysmal hemicrania. The mechanism of this specific action is not fully understood, although an interaction with nitric oxide signaling pathways has been suggested. Trigeminovascular neurons were activated by dural electrical stimulation, systemic administration of a nitric oxide donor, or local microiontophoresis of L-glutamate. Using electrophysiological techniques, we subsequently recorded the activation of trigeminovascular neurons and their responses to intravenous indomethacin, naproxen and ibuprofen. Administration of indomethacin (5 mgkg), ibuprofen (30 mgkg) or naproxen (30 mgkg) inhibited dural-evoked firing within the trigeminocervical complex with different temporal profiles. Similarly, both indomethacin and naproxen inhibited L-glutamate-evoked cell firing suggesting a common action. In contrast, only indomethacin was able to inhibit nitric oxide-induced firing. The differences in profile of effect of indomethacin may be fundamental to its ability to treat paroxysmal hemicrania and hemicrania continua. The data implicate nitric oxide-related signaling as a potential therapeutic approach to these disorders.