Background: Despite significant advances in unravelling the pathophysiology of cluster headache (CH), little is known about neuropsychological functioning. Apart from neuroimaging studies indicating involvement of posterior hypothalamic and other areas frequently involved in nociception, some studies suggest involvement of prefrontal areas. Among others, these mediate executive functioning (EF). Methods: Therefore, three neuropsychological tests (Trail Making Test (TMT), Go/Nogo Task and Stroop Task) were completed by four headache patient samples (chronic CH, episodic CH in the active or inactive period, and migraine patients) and compared to healthy controls. Results: Analyses revealed that patients especially with chronic and active episodic CH were particularly impaired in tests relying more on intact EF (i.e. TMT-B, Stroop interference) than on basal cognitive processes (i.e. TMT-A, Stroop naming). Within the CH groups performance decreased linearly with increasing severity. Discussion: These findings are in line with a recently proposed involvement of prefrontal structures in CH pathophysiology as patients performed worse on neuropsychological tasks relying on these structures. Impaired EF could also result from medication and sleep disturbances due to active CH. Because the decreased performance was also present outside the attacks it may hint at generally altered brain functions, but do not necessarily reflect clinically relevant behaviour.