Prolonged intubation often leads to laryngeal injuries such as subglottic stenosis (SGS), especially in neonates with prematurity and congenital defects key for tissue healing. Recognizing at risk patients in the neonatal intensive care unit (NICU) is not well studied. The study's goals were to determine intubation risk factors, characterize laryngeal injuries, and calculate the incidence of intervention. Retrospective case review. Quaternary pediatric referral center. This retrospective study included all intubated patients in the NICU from April 1, 2020 to 2023. Electronic records were reviewed for demographics and intubation details. Patients were categorized to into intubation only or intervention groups, including direct laryngoscopy and bronchoscopy (DLB) and tracheostomy history. A total of 441 patients were identified with 94 (21%) neonates undergoing DLB. Characteristics impacting intervention included older gestational age, genetic syndromes, and congenital heart disease. Significant risk factors were older age at first intubation, recurrent intubation events, longer intubation duration, and larger endotracheal tube (ETT) diameter, but not birth weight or intubation attempts. Otolaryngology was more likely to intubate the intervention cohort. SGS overall incidence was 2.95% with balloon dilation in 6.4%. Two-thirds of neonates with DLB ultimately required tracheostomy, in which all variables remained significant risk factors except for gestational age. Older age at first intubation, more intubation events, longer intubation duration, and larger ETT increased risk for future DLB and tracheostomy but not birth weight or number of intubation attempts. Most NICU patients selected for DLB ultimately required further procedures.