AimThere are no recommended guidelines or clinical studies on safety of COVID‐19 vaccines in patients with inborn errors of metabolism (IEMs). Here, we aimed to examine the relationship between COVID‐19 vaccination and metabolic outcome in paediatric IEM patients.MethodsPatients with IEM between the ages of 12 and 18 were enrolled. Term metabolic decompensation was defined as acute disruption in metabolic homeostasis due to vaccination. Clinical and biochemical markers were compared between pre‐ and post‐vaccination periods.ResultsData from a total of 36 vaccination episodes in 18 patients were included. Thirteen patients had intoxication‐type metabolic disorders including organic acidemia (OA), urea cycle disorders (UCDs), maple syrup urine disease (MSUD) and phenylketonuria (PKU); 4 patients had energy metabolism disorders including fatty acid metabolism disorders and LIPIN 1 deficiency; and 1 patient had glycogen storage disorder (GSD) type 5. Seventeen patients received BNT162b2, and 1 received CoronaVac because of an underlying long QT syndrome. Fatty acid metabolism disorders, LIPIN 1 deficiency and GSD type 5 were included in the same group named ‘metabolic myopathies’. In two PKU patients, plasma phenylalanine level increased significantly within 24 h following the second dose of vaccination. None of the OA, UCD, MSUD and metabolic myopathy patients experienced acute metabolic attack and had emergency department admission due to metabolic decompensation within 1 month after vaccination.ConclusionsCOVID‐19 vaccines did not cause acute metabolic decompensation in a cohort of 18 children with IEM.