Molybdenum cofactor deficiency is an extremely rare and fatal metabolic disorder that should be considered in the differential diagnosis of hypoxic-ischemic encephalopathy. Magnetic resonance imaging findings are useful in diagnosis. The short-echo-time magnetic resonance spectrum was characterized by a total loss of signal and lipid and lactate peaks. In this case, conventional magnetic resonance imaging and magnetic resonance spectroscopy findings of this extremely rare disease whose pathophysiology was not known were presented.