Fructose-1,6-bisphosphatase (FBPase) deficiency is a rare inborn error of metabolism affecting gluconeogenesis caused by FBP1 gene mutations. It could be more fatal to infants and children when glycogen reserves are insufficient. A 4-year-old girl was admitted with complex febrile convulsion. Initial laboratory results showed hypoglycemia, metabolic acidosis, and hyperlactatemia. Plasma amino acid and urine organic acid analyses showed increased levels of alanine and tricarboxylic acid cycle intermediates. However, she had similar clinical features, including confusion under severe hypoglycemia, two additional times over 6 months. Correct diagnosis could not be made because of nonspecific symptoms, and mitochondrial disorder was initially suspected. Clinical exome sequencing was performed, and compound heterozygous mutations of c.960_961insG and c.490G>A (p. Ser321ValfsTer13 and p. Gly164Ser) in the FBP1 gene were identified. This is the first Korean pediatric case of FBPase deficiency that initially presented with neurologic clinical features. Despite its very low prevalence in Far-East Asian countries, FBPase deficiency should be considered in children with repeated clinical features of metabolic acidosis with hypoglycemia.