Very Low-Calorie Ketogenic Diets (VLCKD) are indicated as a valid tool to treat morbid obesity. Growing evidence suggests an association between overweight/obesity and migraine symptoms and shows how a weight reduction improve pain and headache in these patients. This case report describes the clinical management of a patient affected by obesity, migraine, and celiac disease with a 6-month VLCKD supplemented with a probiotic. The nutritional intervention allowed a significant weight reduction and improvement of migraine symptoms, while being safe and suitable in the setting of a celiac disease.