Background Hospitalized pediatric patients are at an increased risk of experiencing potential drug-drug interactions (pDDIs) due to polypharmacy and the unlicensed and off-label administration of drugs. The aim of this study is to characterize clinically significant pDDIs in pediatric patients hospitalized in a tertiary respiratory center. Methods A retrospective analysis of medications prescribed to pediatric patients admitted to the pediatric ward (PW) and pediatric intensive care unit (PICU) of a respiratory referral center was carried out over a six-month period. The pDDIs were identified using the Lexi-Interact database and considered as clinically relevant according to the severity rating as defined in the database. Frequency, drug classes, mechanisms, clinical managements, and risk factors were recorded for these potential interactions. Results Eight hundred and forty-five pDDIs were identified from the analysis of 176 prescriptions. Of the total pDDIs, 10.2% in PW and 14.6% in PICU were classified as clinically significant. Anti-infective agents and central nervous system drugs were the main drug classes involved in clinically significant pDDIs as object and/or precipitant drugs. A higher number of medications [odds ratio (OR): 4.8; 95% confidence interval (CI): 2.0-11.4; p < 0.001] and the existence of a nonrespiratory disease, which led to a respiratory disorder (OR: 3.8; 95% CI: 1.40-10.4; p < 0.05), were the main risk factors associated with an increased incidence of pDDIs. Conclusions A high and similar risk of pDDIs exists in pediatric patients with respiratory disorders hospitalized in PW and PICU. The patients prescribed a higher number of medications and presenting respiratory symptoms induced by a nonrespiratory disease require extra care and monitoring. Pediatricians should be educated about clinically significant DDIs for highly prescribed medications in their settings in order to take preventive measures and safeguard patient safety.