Evidence suggests that migraine is associated with metabolic syndrome, which is also implicated in non-alcoholic fatty liver disease (NAFLD). Reported for the first time, we aimed to investigate the relationship between migraine and NAFLD in patients with migraine. A total of 90 consecutive migraine patients were enrolled in this cross-sectional study. The diagnosis of migraine was determined according to the International Classification of Headache Disorders-II diagnostic criteria. The diagnosis of NAFLD was based on abdominal ultrasonography findings. Anthropometric indices and the homeostasis model assessment of insulin resistance (HOMA-IR) were calculated, and serum insulin level measurements and other biochemical analyses were performed for each subject. The measurements of body mass index and waist circumference were significantly higher in migraine patients with NAFLD than in those without NAFLD (p < 0.001). Regarding the laboratory results, insulin (p = 0.024), alanine aminotransferase (p = 0.027), and triglyceride levels (p = 0.001) and the HOMA-IR (p = 0.039) were higher in migraineurs with NAFLD than in those without NAFLD. Among the headache characteristics, the presence of aura was higher, and disease and attack durations were significantly longer in migraineurs with NAFLD than in those without NAFLD (p = 0.005, p = 0.024, and p = 0.023; respectively). However, the headache characteristics did not correlate with either the hepatosteatosis grade or HOMA-IR in migraine patients (p > 0.05). Our results show that NAFLD may present in migraine patients with higher frequency of auras and longer disease and attack durations.