Carnitine palmitoyltransferase II (CPT-2) deficiency is a rare and autosomal recessive disorder of long-chain fatty acids oxidation. Here, we reported a 10-year-old boy with bilateral hearing loss and a myopathic form of CPT II deficiency, which was confirmed by a molecular genetic test. He was admitted to our hospital with unexplained headaches, vomiting, and fever. Furthermore, he developed seizures, muscle weakness, neck stiffness and pain, mild respiratory distress, and an icteric appearance. The laboratory test results also showed severely elevated lactate dehydrogenase levels (LDH) and creatine phosphokinase (CPK) levels. He also had an icteric appearance with unexplained indirect hyperbilirubinemia. Further examinations revealed a normal heart and liver without any neurological disorders. Muscle pathological examination reported normal pathology without neuromuscular and mitochondrial disorders and storage diseases. Finally, molecular test analysis with next-generation sequencing (NGS) revealed CPT-II deficiency fatty acid oxidation disorder. Furthermore, we identified a homozygous pathogenic variant in the gene, c.15736C>T p. (Arg5246*), which suggests the Usher syndrome type 2C and the reason for sensorineural hearing loss in this case. Our finding indicates that CPT-II can be associated with multiple symptoms and clinical features. Therefore, evaluation of CPT-II deficiency with molecular test analysis may be helpful in cases with unexplained icteric appearance, muscle weakness, and rhabdomyolysis.