Background Migraine is a common and debilitating neurological disorder characterized with episodic attacks. Epicardial fat is metabolically active and is an important predictor of metabolic and vascular diseases. We aimed to examine whether the echocardiographic measurement of epicardial fat thickness (EFT) and carotid intima-media thickness (CIMT) is increased in patients with episodic migraine (EM). Methods We studied 96 volunteers, including 48 patients with EM (mean age 40.10 +/- 10 years, 41 female patients) and 48 healthy subjects (mean age 42.69 +/- 10 years, gender is the same). All necessary biochemical parameters were analyzed; subsequently, EFT and CIMT were measured in all subjects. The migraine characteristics of the patients were questioned in detail. Results The patients with EM had a significantly higher EFT than the control group (5.34 +/- 1.02 vs. 4.41 +/- 0.68; P < 0.001) and CIMT was also found to be high (median 6.70 vs. 5.60; P < 0.001). Furthermore, there was a positive correlation between EFT and duration of disease and monthly frequency (r = 0.730; P < 0.001). EFT was significantly correlated with CIMT in the migraineurs (P < 0.001). As an optimal cut-off point, a high-risk EFT value of 5.54 mm was determined to predict EM, with 58.3% sensitivity and 96.8% specificity. Conclusion We found that EFT and CIMT were significantly higher in EM patients than in healthy individuals. Increased EFT may be a new risk factor in migraine patients especially in patients with increased pain frequency.