Mitochondrial diseases are a common cause of inherited neurological disorders in children. Although dysfunction of the central nervous system is prominent, multisystem involvement also occurs. Diagnosis relies on characteristic clinical features, an understanding of mitochondrial genetics, and a logical, informed approach to investigations. There is a significant body of recent literature on advances in mitochondrial genetics and the investigation of mitochondrial diseases. However, to our knowledge there remains a paucity of published information on the management of these disorders. Management of the complex constellation of neurological and multisystem clinical features is challenging, and is reliant on a multidisciplinary approach. The care of the child and family is dependent on clear communication between health professionals from primary, secondary, and tertiary care as well as specialist input from quaternary services. The aim of this review is to provide paediatric neurologists, paediatricians, and allied health professionals with a structured approach to the diagnosis and management of children with suspected or confirmed mitochondrial disease.