Patients with refractory epilepsy from inborn errors of metabolism typically present as neonates. Direct supplementation with the deficient vitamin or cofactor is recommended, and case series report both efficacy and safety data of these agents. Some conditions may also occur together, necessitating multiple treatments. Despite effective and early treatment, patients are at heightened risk for neurological sequela. The literature on seizures related to metabolic deficiencies for pediatric patients is limited but has some guidance on appropriate dosing and monitoring for agents to target specific deficiencies, which may help with narrowing antiepileptic therapies, reducing side effects, and improving neurodevelopmental outcomes and quality of life. The focus of this review is to discuss the pharmacotherapy, including the most updated published efficacy and safety data, involved in treating refractory epilepsy as a result of metabolic errors.