Both Sodium Taurocholate Cotransporting Polypeptide Deficiency (NTCPD) and Glycogen Storage Disease Type VI (GSD-VI) are autosomal recessive (AR) genetic disorders that affect liver metabolism in newborns. NTCPD is primarily caused by mutations in the Solute Carrier Family 10 Member 1 (SLC10A1) gene, resulting in decreased bile acid transport function, while GSD-VI is caused by mutations in the phosphorylase glycogen liver (PYGL) gene, leading to a deficiency of liver glycogen phosphorylase. Both diseases are rare, and there have been no previous reports of their coexistence in a single patient. This case report details the rare occurrence of NTCP and GSD-VI in a 2-year-11-month-old female child. The patient presented with mild jaundice, hepatomegaly, and growth retardation. After 1 year and 6 months of treatment and follow-up, the patient's liver function and growth showed significant improvement. This case highlights the importance of comprehensive genetic analysis in diagnosing complex metabolic disorders.