Abstract: Behcet’s disease involves several systems in the body. Neurological involvement is identified by different symptoms. Headache is one of the common complaints of patients with Behcet’s disease. It might be a part of neurological involvement or may arise independently in the course of disease. Studies with small sample size have resulted in various findings in this field. Since the prevalence of Behcet’s disease is relatively high in Iran, this study was carried out to compare the features of headache between an acceptable number of patients with this rare disease and a control group. Methods: The current case–control study was performed to compare the features of headache between 312 patients with definite Behcet’s disease who referred to a Behcet’s clinic and healthy individuals. Patients with Behcet’s disease were randomly selected. Controls were matched for age and sex. They were personally examined and interviewed meticulously using a questionnaire that met the standards of the International Headache Society classification for different types of headache. Results: The incidence of headache in the case and control groups was 28.3 % (n = 120) and 18.6 % (n = 59), respectively (p < 0.05; OR 2.73). Tension-type headache was observed in 12.2 % (n = 38) of cases which was significantly higher than control group (n = 6.3 %) (p = 0.011; OR 2.05). The most frequent type of headache in the case group was tension-type headache (12.2 %). In the control group, however, migraine without aura was the most common type (9.1 %). A correlation between ophthalmological involvement and headache was observed in 11 patients in the case group. In addition, a significantly higher systolic blood pressure was found in the case group compared to the controls (125.1 vs. 121.7 mmHg; p = 0.007). There was no major correlation between prednisolone consumption in patients with Behcet’s disease and the type and frequency of headache. Conclusions: Headache, especially tension-type headache, is more common in patients with Behcet’s disease. This might be the result of specific types of uveitis-related and non-structural headaches seen in Behcet’s disease.