In recent years, there has been an increasing knowledge in the pathogenesis and better management of chronic headaches. Current scientific evidence supports the role of manual therapies in the management of tension type and cervicogenic headache, but the results are still conflicting. These inconsistent results can be related to the fact that maybe not all manual therapies are appropriate for all types of headaches; or maybe not all patients with headache will benefit from manual therapies. There are preliminary data suggesting that patients with a lower degree of sensitization will benefit to a greater extent from manual therapies, although more studies are needed. In fact, there is evidence demonstrating the presence of peripheral and central sensitization in chronic headaches, particularly in tension type. Clinical management of patients with headache needs to extend beyond local tissue-based pathology, to incorporate strategies directed at normalizing central nervous system sensitivity. In such a scenario, this paper exposes some examples of manual therapies for tension type and cervicogenic headache, based on a nociceptive pain rationale, for modulating central nervous system hypersensitivity: trigger point therapy, joint mobilization, joint manipulation, exercise, and cognitive pain approaches.