Introduction: Epilepsy is one of the leading chronic diseases of childhood, and an underlying IEM is an etiology that can easily be overlooked. The aim of this study was to determine the frequency of metabolic disease in patients diagnosed with epilepsy in the first two years of life, as well as to determine the clinical, radiological, and electroencephalographic (EEG) characteristics of the metabolic disease subtypes associated with epilepsy and evaluate treatment response in our study. Materials and methods: The records of patients diagnosed with epilepsy before the age of 2 years in our pediatric neurology clinic between 2014 and 2021 were reviewed retrospectively. Those diagnosed with an IEM and followed up in the pediatric neurology and pediatric metabolism departments of our hospital were included in the study. Results: A total of 990 patients under the age of 2 years were diagnosed with epilepsy in the pediatric neurology clinic of our hospital and 74 (7.5%) of them had IEM. Thirty-nine (52.7%) of the 74 patients were female. The median age at admission was 144 days (min–max: 0–284). Of the 74 patients diagnosed with metabolic epilepsy, 38 patients were diagnosed with amino acid metabolism disorder, 17 with lysosomal storage disease, 9 with energy metabolism disorder, 5 with vitamin/cofactor/trace element metabolism disorders, 2 with fatty acid metabolism disorder, 2 with peroxisomal disease, and 1 with carbohydrate metabolism disorder. Epilepsy was refractory despite appropriate treatment in 39 patients (52.7%). Conclusion: Inborn errors of metabolism are a rare cause of epilepsy, in regions like our country with high rates of consanguineous marriage, IEM should be considered in patients presenting with seizures that do not respond to conventional antiepileptic treatments.