We aimed to explore parents’ perceptions of their children’s medication use for inborn errors of metabolism (IEM), including the importance of medication intake, potential complications, and concerns about adverse drug reactions (ADR). Additionally, we aimed to determine expert-assessed clinically relevant drug-related problems, particularly those attributable to IEM. We interviewed 108 parents of 119 pediatric patients with IEM using a questionnaire relating to their perceptions regarding their children’s IEM medication. In affected siblings, a questionnaire was used for each child. We performed medication analyses to evaluate the patient’s complete medication regimen for clinically relevant drug-related problems, including medication for conditions other than IEM. It was very important to the parents of 85% of the patients to use IEM medication exactly as prescribed. The parents of 41% of patients perceived complications in their children’s use of IEM medication. The parents of 47% of patients reported fears concerning ADR because of IEM medication. Parents observed ADR in 27% of patients because of IEM medication. In 44% of patients, medication for conditions other than IEM was inadequate because of drug-related problems not associated with the IEM; a safe alternative existed in 21% of patients. In summary, almost half of the parents of patients with IEM reported complications with their child’s IEM medication intake and fears of ADR. Medication analyses showed that drug-related problems occurred regardless of IEM, emphasizing the general need to prescribe and dispense adequate, child-appropriate medication to minimize clinically relevant drug-related problems in pediatric patients.