In this prospective study, we aimed to determine the prevalence of migraine and non-migraine headaches using a questionnaire, including ID Migraine™, for university students. The study was designed cross-sectionally and a questionnaire consisting of 43 questions was applied to 1,256 students. The questionnaire consisted of questions related to demographic, social, curriculum, housing and headache characteristics of the subjects. Three-item screening questions of the ID Migraine™ test were included at the end of the questionnaire aimed at migraine diagnosis. The mean age of 1,256 students (529 females and 727 males) enrolled in this study was 21.9 ± 2.1 years (17–31 years). Migraine-type headache was detected in 265 subjects (21.9%) based on the ID Migraine™ evaluation. Of these, 145 (54.7%) were female and 120 (45.3%) were male (female/male ratio: 1.2/1). Non-migraine-type headache was identified in 864 subjects, with 357 females and 507 males. As a conclusion, ID Migraine™ screening test might be practical and beneficial when a face-to-face interview is not possible or to pre-determine the subjects for a face-to-face interview for migraine diagnosis in larger populations.