Primary headaches (PHAs) prominently affect the performance and life quality of people. Sexual dysfunction (SD) is an important health problem caused by several factors. This study aimed to compare the sexual function of women who have PHAs. Forty-one female patients who were diagnosed with migraine, 39 female patients who were diagnosed with tension-type headache (TTHA) and 41 healthy subjects were included in study. Sexual function of the cases were evaluated by using the ‘Female Sexual Function Index (FSFI)’. Beck Depression Scale was applied to subjects and those who were diagnosed with depression were excluded from the study. SD was detected in both the migraine and TTHA groups. FSFI subgroup scores were statistically significantly lower in the migraine and TTHA groups compared with the control group. No significant differences were detected between the migraine and TTHA groups in terms of FSFI and its components. In addition, no significant differences were detected between the blood prolactin levels or SD and headache. It was concluded that primary headaches (which are chronic diseases) itself may cause SD in female patients with migraine and TTHA independently of factors that may cause development of SD such as comorbid condition, depression, drug use and age.