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Introduction Nearly half of neonatal intubations are complicated by severe desaturation (≥20% decline in pulse oximetry saturation (SpO2)). Apnoeic oxygenation prevents or delays desaturation during intubation in adults and older children. Emerging data show mixed results for apnoeic oxygenation using high-flow nasal cannula (NC) during neonatal intubation. The study objective is to determine among infants ≥28 weeks’ corrected gestational age (cGA) who undergo intubation in the neonatal intensive care unit (NICU) whether apnoeic oxygenation with a regular low-flow NC, compared with standard of care (no additional respiratory support), reduces the magnitude of SpO2 decline during intubation.Methods and analysis This is a multicentre, prospective, unblinded, pilot randomised controlled trial in infants ≥28 weeks’ cGA who undergo premedicated (including paralytic) intubation in the NICU. The trial will recruit 120 infants, 10 in the run-in phase and 110 in the randomisation phase, at two tertiary care hospitals. Parental consent will be obtained for eligible patients prior to intubation. Patients will be randomised to 6 L NC 100% oxygen versus standard of care (no respiratory support) at time of intubation. The primary outcome is magnitude of oxygen desaturation during intubation. Secondary outcomes include additional efficacy, safety and feasibility outcomes. Ascertainment of the primary outcome is performed blinded to intervention arm. Intention-to-treat analyses will be conducted to compare outcomes between treatment arms. Two planned subgroup analyses will explore the influence of first provider intubation competence and patients’ baseline lung disease using pre-intubation respiratory support as a proxy.Ethics and dissemination The Institutional Review Boards at the Children’s Hospital of Philadelphia and the University of Pennsylvania have approved the study. Upon completion of the trial, we intend to submit our primary results to a peer review forum after which we plan to publish our results in a peer-reviewed paediatric journal.Trial registration number ClinicalTrials.gov Registry (NCT05451953).