Headache is one of the chronic disorders that can trigger sexual dysfunction due to complex mechanisms. This study recruited 120 consecutive patients from our outpatient clinics with migraine (n = 60), TTH (n = 60) as well as healthy age-matched controls (n = 60) for a total of 180 patients. All the participants were evaluated by the Arabic version of the female sexual function index (ArFSFI: 19 items), the abridged 5-item version of the international index of erectile function (IIEF-5), hospital anxiety and depression scale (HADS: 14 items), visual analog scale (VAS) score, and the headache impact test questionnaire (HIT-6TM: 6 items). A significant correlation was noticed between scores of total ArFSFI in women with TTH and their partners’ IIEF-5 scores (r = 0.773, p < 0.001). In contrast, significant negative correlations were also found between scores of total ArFSFI in women with migraine(r – 0.327, p 0.011), HADS-A scores (r – 0.504, p < 0.001), HADS-D scores (r – 0.579, p < 0.001), HITS scores (r – 0.413, p 0.001), VAS scores (r 0.737, p < 0.001), and their partners' IIEF-5 scores (r – 0.839, p < 0.001). Interestingly, our study had shown a bidirectional relation between SD, anxiety, and depression subscales of HADS in females with migraine only (28.49 ± 9.46, 13.54 ± 4.44, 15.17 ± 7.73 respectively, p 0.009), while females with migraine and SD reported statistical higher scores of anxiety and depression (25.21 ± 11.70, 12.71 ± 4.20, 17.95 ± 8.05, respectively, p 0.006). This study had demonstrated that drug-naïve Egyptian females with migraine are more prone to SD than those with TTH.