Hereditary fructose intolerance (HFI) can present in neonates due to hidden fructose/sucrose in infant formulas, causing acute liver failure. This case report describes a 17-day-old formula-fed infant diagnosed via expedited whole exome sequencing (WES) in 5 days, with rapid recovery after switching to fructose-free formula. Clinicians should consider HFI in neonatal acute liver failure and utilize rapid genomic testing for early diagnosis.