Molybdenum cofactor deficiency is a rare neurometabolic disease that is usually characterized by seizures, abnormal muscle tonus, developmental delay and poor nutrition, and is seen soon after birth. Pyloric stenosis causes serious vomiting in the first months of life. The presence of neurologic damage in molybdenum cofactor deficiency and possible abnormal innervations may cause pyloric stenosis; however, the pathogenesis is unclear. Pyloric stenosis with molybdenum cofactor deficiency has been described in two cases. Herein, we report the third case and suggest that hypertrophic pyloric stenosis should be kept in mind as a clinical manifestation of molybdenum cofactor deficiency.