Parainfluenza virus infection is one of the causes of fatal rhabdomyolysis. Rhabdomyolysis can be aggravated by mitochondrial fatty acid beta-oxidation disorders during prolonged periods of fasting. Moreover, in patients with late-onset isovaleric acidemia, hyperammonemia may occur following catabolic stress. In the present report, we describe a case of a 4-year-old boy with parainfluenza virus infection and late-onset isovaleric acidemia that rapidly progressed to coma, seizures, and cardiorespiratory collapse. His serum ammonia and creatinine kinase (CK) levels were 385 microMol/L and 23,707 IU/L, respectively. Continuous renal replacement therapy (CRRT) was initiated using continuous venovenous hemodiafiltration, after which the ammonia and CK levels returned to normal. Thus, we recommend the immediate initiation of CRRT in the management of patients with life-threatening rhabdomyolysis and hyperammonemia.