Benjamin Sisko suffers severe headaches in 2373
A headache is classed as a mild to severe pain in the head. It's causes were often vascular. (ENT: "Observer Effect") Medical advances made headaches uncommon or rare by the 24th century. (TNG: "The Battle")
Captain Kirk complained of a headache during the encounter with the Klingons at Deep Space Station K-7. Upon arriving in sickbay, Dr. McCoy provided a pill, and asked whether the headache was due to Baris or the Klingons. This suggests that stress-induced headaches were still common in the 2260s. (TOS: "The Trouble with Tribbles")
Captain Picard experienced a headache when he was under the influence of a thought maker. (TNG: "The Battle")
Early stages of the loss of her empathic sense due to the presence of the two-dimensional lifeforms were massive headaches, experienced by Deanna Troi. (TNG: "The Loss")
Doctor Julian Bashir experienced headache after the consciousness from the Kobliad criminal Rao Vantika was beamed out of his brain. (DS9: "The Passenger")
Elim Garak experienced headaches prior to his collapse in Quark's in 2370. (DS9: "The Wire")
While in close proximity to a type-4 quantum singularity in 2371, a number of crewmembers of the USS Voyager reported to sickbay with headaches, including Ensign Harry Kim. (VOY: "Parallax")
Benjamin Sisko suffered severe headaches in 2373 following exposure to a plasma burst from a holosuite console. The headaches were associated with odd synaptic potentials and post-neural shock syndrome, and also with a series of prophetic visions. Eventually, a neuropolaric induction was required to correct the condition. (DS9: "Rapture")
Kathryn Janeway also experienced continuous headaches when the Srivani were performing experiments on her regarding how well she could handle stress and pain. (VOY: "Scientific Method")