Thoracic surgery and one-lung ventilation in young children carry significant risks. Approaches to one-lung ventilation in young children include endobronchial intubation (mainstem intubation) and use of a bronchial blocker. We hypothesized that endobronchial intubation is associated with a greater prevalence of airway complications compared to use of a bronchial blocker. The Multicenter Perioperative Outcomes Group database was queried from 2004 to 2022 for one-lung ventilation cases in children, 2 months to 3 years of age, inclusive. Airway notes and free-text comments were manually reviewed for airway complications. Documented airway complications were considered the primary outcome and were divided into "Moderate" and "Critical." Moderate airway complications were bronchial blocker or endotracheal tube movement leading to loss of isolation, hypoxemia requiring ventilatory intervention, bronchial blocker migration into the trachea, significant impairment of ventilation, and other. Critical complications included reintubation or airway replacement intraoperatively, complete endotracheal tube occlusion, cardiac arrest or airway-related bradycardia, and procedure aborted due to an airway issue. An adjusted propensity score-matched analysis was then used to assess the impact of a bronchial blocker on the outcomes of moderate and critical complications. After exclusions, 704 patients were included in the primary analysis. In unadjusted analyses, no statistically significant difference was observed in moderate airway complications between endobronchial intubation and bronchial blocker cohorts: 37 of 444 (8.3%; 95% confidence interval [CI], 5.9%-11.3%) vs 28 of 260 (10.8%; 95% CI, 7.3%-15.2%) with P = .281. In the unadjusted analysis, the prevalence of critical airway complications was significantly higher in the endobronchial intubation cohort compared to the bronchial blocker cohort: 28 of 444 (6.3%; 95% CI, 4.2%-9.0%) vs 5 of 260 (1.9%; 95% CI, 0.6%-4.4%) with P = .008. In the propensity-matched cohort analysis, endobronchial intubation was associated with a slightly increased risk of critical complications compared to use of a bronchial blocker: 14 of 243 (5.8%; 95% CI, 2.8%-8.7%) vs 5 of 243 (2.1%; 95% CI, 0.3%-3.8%) with P = .035. Endobronchial intubation might be associated with a slightly increased risk of critical airway complications compared to use of a bronchial blocker in young children undergoing thoracic surgery and one-lung ventilation. Further, prospective studies are needed before a definitive change in practice is recommended.