Background: Generating evidence to inform care for pediatric medium-chain acyl-CoA dehydrogenase (MCAD) deficiency requires sustainable and integrated measurement of priority outcomes. Methods: From an existing Canadian cohort study, we evaluated the quality of metabolic clinic chart-abstracted data for measuring core outcomes for pediatric MCAD deficiency. We then modelled variation in emergency department (ED) use, in association with disease severity, child age, and distance to care. Results: Children with MCAD deficiency visit the metabolic clinic at least annually on average but we identified data quality challenges related to inconsistent definitions of core outcomes and missing information in patient charts. Rates of ED use were highest among children aged 6 to 12 months, with more severe disease, and living closest to care. Conclusion: While measuring core outcomes through the metabolic clinic for children with MCAD deficiency is feasible, harmonized data collection is needed to evaluate care and further understand ED use.