Cuffed endotracheal tubes (ETTs) are becoming increasingly used in neonates; nevertheless, current data in the literature mostly include infants over 3,000 g in weight. The aim of this study was to compare the use of cuffed and uncuffed ETTs in neonates in the neonatal intensive care unit of a tertiary children's hospital, assessing the presence of airway complications. We performed a single-center retrospective cohort study. Our study included all term neonates receiving cuffed ETTs over the period from January 2019 to December 2021. The controls were all neonates receiving an uncuffed ETT over the same period. Twenty-five patients were intubated with cuffed ETTs in the study period. The group receiving cuffed ETTs was compared with 53 patients receiving uncuffed ETTs. All cuffed ETTs were inserted in the operating room by anesthesiologists. Comparing the outcomes of the cuffed ETT group with controls, there were no significant differences in the number of unplanned extubations, reintubation episodes, ventilator-associated pneumonia, episodes of atelectasis, the use of dexamethasone, or vocal cord paresis. No unplanned extubation was observed in the cuffed ETT group, and no cases of subglottic stenosis were observed in either of the groups. This retrospective study with a small sample size suggests that the use of cuffed ETTs in surgical patients >2,000 g in weight is not associated with an increase in airway complications. Well-designed randomized controlled trials are needed to compare cuffed ETTs with uncuffed ETTs.