Molybdenum cofactor deficiency (MoCD) is a rare autosomal recessive disorder that may present during the neonatal period with intractable seizures. Co-existence of MoCD and pyloric stenosis is previously reported as a coincidence or common etiology. The etiology of the two conditions is unclear; however, reports demonstrate neuronal deficiency in both. We report a neonate who was diagnosed with MoCD and hypertrophic pyloric stenosis.