A full-term male neonate, aged 2 days, was admitted for jaundice lasting more than 2 days. On the day of admission, he developed sudden respiratory arrest and shock; vital signs were restored after active resuscitation. The acylcarnitine profile showed markedly elevated long-chain acylcarnitines, including C16∶1, C18, and C18∶1, indicating a fatty acid oxidation disorder and raising suspicion for carnitine-acylcarnitine translocase deficiency or carnitine palmitoyltransferase II deficiency. Whole-exome sequencing identified compound heterozygous variants in SLC25A20: c.823C>T (p.Arg275Ter) and c.199-10T>G, classified as likely pathogenic and pathogenic, respectively, confirming carnitine-acylcarnitine translocase deficiency. On day 50 of life, infection precipitated a metabolic crisis with recurrent shock; considering the poor prognosis, the family chose to withdraw treatment, and the patient died on day 52 of life. Carnitine-acylcarnitine translocase deficiency is a congenital fatty acid oxidation disorder. Neonatal fatty acid oxidation disorders typically have acute onset, rapid progression, and atypical manifestations, predisposing to misdiagnosis and poor prognosis. This case may serve as a reference for the clinical recognition and management of neonatal fatty acid oxidation disorders.