Acute encephalopathy with biphasic seizures and late reduced diffusion (AESD) is difficult to differentiate from prolonged febrile seizures during the acute phase. Mitochondrial dysfunction-induced energy depletion is among the key mechanisms underlying acute encephalopathy. Therefore, this study aimed to examine the efficacy of a “mitochondrial cocktail” in preventing AESD. We retrospectively studied children experiencing status epilepticus associated with fever lasting more than 30 min, focusing on those who received the mitochondrial cocktail between February 2016 and December 2020, and those who did not receive it within 24 h between February 2012 and January 2014. The mitochondrial cocktail contained vitamins B1, C, and E; biotin; coenzyme Q10; and l-carnitine. AESD occurred in 1 of 41 (2.4 %) patients in the administration group and 7 of 39 (17.9 %) patients in the non-administration group. The incidence of AESD was lower in the administration group than in the non-administration group, with a significant difference (p = 0.027). The incidence of encephalopathy, including cases classified as AESD and unclassified, was 7/41 (17.1 %) and 7/39 (17.9 %) in the administration and non-administration groups, respectively, with no significant difference. However, the number of cases with worsening pediatric cerebral performance category scores was significantly lower in the administration group compared to the non-administration group (p = 0.015). In conclusion, early administration of the mitochondrial cocktail may help prevent AESD. Some encephalopathy cases do not progress to a biphasic state or develop AESD. Thus, the mitochondrial cocktail should be administered as early as possible to prevent AESD.