To our knowledge, a patient with recurrent syncope due to vitamin B12 deficiency without hematologic manifestations has not been reported before. We present the case of an 83-year-old man who experienced a third episode of syncope, characterized by sudden loss of consciousness without convulsions and rapid recovery. His medical history included ischemic stroke 22 years earlier and multiple bowel resections following cholecystectomy 21 years ago. The examination revealed a severe vitamin B12 deficiency and bradycardia on ECG. The examination for heart disease was inconclusive. The syncope was attributed to a vitamin B12 deficiency and consecutive cardiac autonomic neuropathy (CAN) after other causes for the syncope were sufficiently ruled out. Syncopes did not recur after adequate vitamin B12 supplementation. This case illustrates that partial bowel resection may lead to severe vitamin B12 deficiency, which can result in CAN. Disturbed autonomic innervation of the cardiac conduction system can lead to bradycardia, which, in turn, can result in syncope. Patients with a history of complete or partial bowel resection should undergo regular monitoring of vitamin B12 levels to prevent potentially symptomatic deficiency.