Phosphoglycerate kinase deficiency (PGK1D) is a rare X-linked metabolic disorder with variable phenotype. Mutations of the PGK1 gene result in clinically variable spherocytic hemolytic anemia and variable defects in the central nervous system. Rhabdomyolysis, myopathy, migraine, and retinal involvement have also been reported as clinical consequences. We describe for the first time the anaesthetic management of a patient with the X-linked phosphoglycerate kinase deficiency scheduled for an open gastrostomy procedure to facilitate enteral nutrition due to chronic oral aversion. Given the various organs systems involved, we suggest a number of preoperative investigations and describe our intraoperative management. Given the paucity of literature regarding children with this condition, we believe this case report will be a worthwhile addition to the anaesthetic literature to help guide other anaesthetists managing patients with this condition.