Background Middle aortic syndrome is a rare disease. Several surgical treatments are available; however, the optimal treatment strategy and long-term outcomes remain unelucidated. We herein report the 5-year outcomes of six patients treated with extra-anatomical bypass surgery for middle aortic syndrome. Case presentations Between 2013 and 2016, six patients underwent extra-anatomical bypass for middle aortic syndrome at our institute: three had Takayasu’s arteritis, one had vessel vasculitis, and two had middle aortic hypoplastic syndrome of unknown origin. The patients included five women and one man, with a mean age of 59.7 years. Four patients had uncontrolled hypertension and were receiving antihypertensive medications. The mean ankle–brachial pressure index was .61. The three patients with Takayasu’s arteritis were hospitalized for congestive heart failure. These patients underwent bypass surgery from the descending aorta to the infrarenal abdominal aorta, and one also underwent concomitant heart surgery. The patient with microscopic polyangiitis underwent Y-grafting with an aortic aneurysmectomy. Subsequently, bypass surgery was performed from the descending aorta to the graft via the diaphragm. The two patients with unknown causes underwent bypass surgery from the proximal descending aorta to the distal descending thoracic aorta. There were no early or late deaths at the 5-year follow-up. We did not observe any changes in anastomotic site stenosis or new aneurysmal changes during the follow-up period. The number of antihypertensive medications was reduced in all cases, and critical symptoms, including headache, severe abdominal pain, claudication, and heart failure, improved in all patients. The ankle–brachial pressure index increased to 1.11 and did not change for five years. Renal function remained stable, and the brain natriuretic peptide level decreased from 302.8 to 74.5 pg/mL at follow-up. Conclusion Extra-anatomical bypass for middle aortic syndrome is safe and effective, and can help prevent renal failure, and relieve critical ischemic symptoms.