Despite advances in pharmacological therapies, migraine patients are often drug resistant. Further therapeutic options in this field are, therefore, desirable. Recent studies have highlighted the efficacy of ketogenic diet (KD) on improving migraine, but data on their long-term efficacy and safety are lacking. In this study, we retrospectively evaluated the long-term effectiveness of the modified Atkins ketogenic diet (MAD) in episodic or chronic drug-resistant migraine patients. 52 patients diagnosed with episodic or chronic drug-resistant migraine under modified Atkins ketogenic diet (MAD) were evaluated. In total, 41 patients followed the diet for 6 months and 33 for 12 months. After both 6 and 12 months, frequency, length, and intensity of migraine episodes, as well as the number of medications significantly decreased with respect to the start of the diet. Body mass index, high sensitivity PCR, diastolic blood pressure, fasting plasma insulin and HOMA index were also significantly reduced both after 6 and 12 months. No major metabolic changes were observed during MAD treatment. In conclusion, KD has been shown to be effective and safe in the long-term treatment of drug-resistant migraine. A high dropout rate still remains an important factor, which often limits its use.