Vitamin D deficiency is a major cause of hypocalcemic seizures in infants. Chronic enteropathy can cause both malnutrition and vitamin deficiency disorders, such as celiac disease, in Western Caucasians. However, gluten-related disorders are considered uncommon in most Asian countries, and there have been no reports of any infant being diagnosed with a gluten-related disorder in Japan. Here, we describe a case where a Japanese infant, with non-celiac gluten sensitivity, presented with hypocalcemic seizures resulting from a vitamin D deficiency. In this case, an eight-month-old boy had an afebrile seizure, and blood tests revealed both hypocalcemia and prolonged prothrombin time resulting in his transfer to our hospital. The presence of fatty stools and evidence of multiple vitamin deficiencies indicated some form of fat malabsorption. His laboratory and histological findings showed enteropathy, and he was thus diagnosed with non-celiac gluten sensitivity. Therefore, he was treated with a gluten-free diet supplemented with vitamins. This case suggests that infants with a vitamin D deficiency caused by celiac disease or non-celiac gluten sensitivity should be carefully monitored when they are given oral supplements of vitamin D, to prevent any adverse side-effects associated with the varied roles of vitamin D in the immune response.