Studies have suggested a possible association of migraine and increased risk of ischemic stroke in young adults, particularly in smokers and in women who use oral contraceptive drugs. We aimed to analyze the association between migraine and ischemic stroke in young population in a hospital-based cohort. We included 202 consecutive patients with the diagnosis of ischemic stroke who were between 15 and 50 years and age- and gender-matched 250 volunteers with no history of stroke. All participants were interviewed using a questionnaire for migraine. Localization of ischemic lesion was classified as anterior and posterior circulation according to neuroimaging findings. The cause of ischemic lesion and all risk factors were recorded. Undetermined etiology was the most frequent (43.1%) and the most common determined cause was cardioembolism (22.3%) in young stroke patients. Frequency of migraine was 30.2% among patients with stroke whereas 16.8% of healthy subjects had migraine (p = 0.001). Migraine with aura was significantly more common among patients with stroke compared to healthy subjects (18.3 vs 4.4%; p = 0.000) whereas the frequency of migraine without aura was similar in both groups (11.9 vs 12.4%). Using logistic regression, migraine with aura was shown to be an independent risk factor for ischemic stroke in young population (p = 0.000) and separate analysis for gender demonstrated that it was only a risk factor for women (p = 0.009) but not for men (p = 0.107). Migraine with aura was found to be more common in ischemic stroke in young patients. It was an independent risk factor in women.