CHARGE syndrome is a rare autosomal dominant disorder involving multiple organs. Chromodomain helicase DNA binding protein-7 (CHD7) is a major causative gene of CHARGE syndrome. We herein report a male infant born at full term with asphyxia who was diagnosed with CHARGE syndrome based on the typical anomalies. He showed a poor sucking ability and suffered from continuous hypoglycemia in early infancy, ultimately requiring tube feeding. While in a hypoglycemic status, inappropriate high insulin and low growth hormone levels were noticed. Growth hormone replacement therapy partially increased his blood glucose levels, but asymptomatic hypoglycemia with hyperinsulinemia was occasionally noticed. Additional diazoxide treatment stabilized his blood level to within the normal range. A genetic analysis of CHD7 showed the novel heterozygous monoallelic mutation c.2990delT causing a reading frameshift p.Leu997Trpfs*15 in exon 12. This case shows that patients with CHARGE syndrome caused by a CHD7 mutation may present with persistent hyperinsulinemic hypoglycemia, just like other dysmorphic syndromes genetically caused by aberrations in chromatin remodeling.