Background Migraine — an episodic headache —is one of the most common types of primary Headache. Migraine is considered a serious health problem that affects the quality of life. During university life, students often report increased levels of stress, depression, anxiety, and irregular sleep, all of which are associated with migraines.Our aim was to determine the prevalence of migraine headaches among medical campus students at university of Khartoum, Sudan. Based on available data, migraine is on the rise in both general populations as well as university students. Methods In this cross-sectional and descriptive study, study population was composed of students registered to faculty of medicine, Dentistry and pharmacy at Khartoum University in the academic years of 2020-2021. Out of these 318 of them accepted to participate. Participants who had two or more headaches in the last 3 months formed the headache group. Afterwards, two preliminary questions were applied to the headache group and participants with at least one affirmative response were asked to perform the validated ID-Migraine™ test. Results The mean age of 318 students participated in the study was 19.23 ± 1.84 (17-39 years), with adolescents: adult ratio being 2.5:1. 1613 students (43.7%) did have at least two headaches in the last three months. Migraine-type headache was detected in 266 subjects (7.2%) based on the ID-Migraine™ test. Of the migraine group, 72 were male (27.1%) and 194 were female (72.9%). There was no significant difference in migraine prevalence between adolescent and adult age groups. Conclusions With prevalence similar to adults, primary care physicians should be aware of the probability of migraine headaches in university students in order to maintain a successful school performance.